Package: src:r-bioc-affxparser
Version: 1.74.0-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
dh_auto_configure -O--buildsystem=R
dh_auto_build -O--buildsystem=R
dh_auto_test -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=R
dh_prep -O--buildsystem=R
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
I: R Package: affxparser Version: 1.74.0
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Wed, 29 Nov 2023 16:03:10 +0100
mkdir -p
/<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library
--clean . "--built-timestamp='Wed, 29 Nov 2023 16:03:10 +0100'"
* installing *source* package ‘affxparser’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++ (Debian 13.2.0-25) 13.2.0’
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f fusion/calvin_files/data/src/CDFData.o
fusion/calvin_files/data/src/CDFProbeGroupInformation.o
fusion/calvin_files/data/src/CDFProbeInformation.o
fusion/calvin_files/data/src/CDFProbeSetInformation.o
fusion/calvin_files/data/src/CDFQCProbeInformation.o
fusion/calvin_files/data/src/CDFQCProbeSetInformation.o
fusion/calvin_files/data/src/CELData.o
fusion/calvin_files/data/src/CHPBackgroundZone.o
fusion/calvin_files/data/src/CHPData.o
fusion/calvin_files/data/src/CHPExpressionEntry.o
fusion/calvin_files/data/src/CHPMultiDataData.o
fusion/calvin_files/data/src/CHPTilingData.o
fusion/calvin_files/data/src/CHPQuantificationData.o
fusion/calvin_files/data/src/CHPQuantificationDetectionData.o
fusion/calvin_files/data/src/CHPGenotypeEntry.o
fusion/calvin_files/data/src/CHPUniversalEntry.o
fusion/calvin_files/data/src/ColumnInfo.o
fusion/calvin_files/data/src/DataGroup.o
fusion/calvin_files/data/src/DataGroupHeader.o
fusion/calvin_files/data/src/DataSet.o
fusion/calvin_files/data/src/DataSetHeader.o
fusion/calvin_files/data/src/FileHeader.o
fusion/calvin_files/data/src/GenericData.o
fusion/calvin_files/data/src/GenericDataHeader.o
fusion/calvin_files/exception/src/ExceptionBase.o
fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o
fusion/calvin_files/fusion/src/FusionBPMAPData.o
fusion/calvin_files/fusion/src/FusionCDFData.o
fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
fusion/calvin_files/fusion/src/FusionCELData.o
fusion/calvin_files/fusion/src/FusionCHPData.o
fusion/calvin_files/fusion/src/FusionProbeSetResults.o
fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
fusion/calvin_files/fusion/src/FusionCHPLegacyData.o
fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o
fusion/calvin_files/fusion/src/FusionCHPTilingData.o
fusion/calvin_files/fusion/src/FusionCHPGenericData.o
fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o
fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o
fusion/calvin_files/parameter/src/ParameterNameValueType.o
fusion/calvin_files/parsers/src/CDFFileReader.o
fusion/calvin_files/parsers/src/CelFileReader.o
fusion/calvin_files/parsers/src/CHPFileReader.o
fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o
fusion/calvin_files/parsers/src/CHPTilingFileReader.o
fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o
fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o
fusion/calvin_files/parsers/src/DataGroupHeaderReader.o
fusion/calvin_files/parsers/src/DataGroupReader.o
fusion/calvin_files/parsers/src/DataSetHeaderReader.o
fusion/calvin_files/parsers/src/DataSetReader.o
fusion/calvin_files/parsers/src/FileHeaderReader.o
fusion/calvin_files/parsers/src/FileInput.o
fusion/calvin_files/parsers/src/GenericDataHeaderReader.o
fusion/calvin_files/parsers/src/GenericFileReader.o
fusion/calvin_files/utils/src/AffymetrixGuid.o
fusion/calvin_files/utils/src/DateTime.o
fusion/calvin_files/utils/src/FileUtils.o
fusion/calvin_files/utils/src/StringUtils.o
fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o
fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o
fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o
fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o
fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o
fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o
fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o
fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o
R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o
R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o 000.init.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFData.cpp
-o fusion/calvin_files/data/src/CDFData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CDFProbeGroupInformation.cpp -o
fusion/calvin_files/data/src/CDFProbeGroupInformation.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CDFProbeInformation.cpp -o
fusion/calvin_files/data/src/CDFProbeInformation.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CDFProbeSetInformation.cpp -o
fusion/calvin_files/data/src/CDFProbeSetInformation.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CDFQCProbeInformation.cpp -o
fusion/calvin_files/data/src/CDFQCProbeInformation.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o
fusion/calvin_files/data/src/CDFQCProbeSetInformation.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CELData.cpp
-o fusion/calvin_files/data/src/CELData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPBackgroundZone.cpp -o
fusion/calvin_files/data/src/CHPBackgroundZone.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
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-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPData.cpp
-o fusion/calvin_files/data/src/CHPData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
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-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
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-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPExpressionEntry.cpp -o
fusion/calvin_files/data/src/CHPExpressionEntry.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
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-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
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-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
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-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPMultiDataData.cpp -o
fusion/calvin_files/data/src/CHPMultiDataData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
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-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
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-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPTilingData.cpp -o
fusion/calvin_files/data/src/CHPTilingData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
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-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
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-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
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-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPQuantificationData.cpp -o
fusion/calvin_files/data/src/CHPQuantificationData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
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-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
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-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o
fusion/calvin_files/data/src/CHPQuantificationDetectionData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
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-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPGenotypeEntry.cpp -o
fusion/calvin_files/data/src/CHPGenotypeEntry.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/CHPUniversalEntry.cpp -o
fusion/calvin_files/data/src/CHPUniversalEntry.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/ColumnInfo.cpp -o fusion/calvin_files/data/src/ColumnInfo.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataGroup.cpp
-o fusion/calvin_files/data/src/DataGroup.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/DataGroupHeader.cpp -o
fusion/calvin_files/data/src/DataGroupHeader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataSet.cpp
-o fusion/calvin_files/data/src/DataSet.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/DataSetHeader.cpp -o
fusion/calvin_files/data/src/DataSetHeader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/FileHeader.cpp -o fusion/calvin_files/data/src/FileHeader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/GenericData.cpp -o fusion/calvin_files/data/src/GenericData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/data/src/GenericDataHeader.cpp -o
fusion/calvin_files/data/src/GenericDataHeader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/exception/src/ExceptionBase.cpp -o
fusion/calvin_files/exception/src/ExceptionBase.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o
fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o
fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionBPMAPData.cpp -o
fusion/calvin_files/fusion/src/FusionBPMAPData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCDFData.cpp -o
fusion/calvin_files/fusion/src/FusionCDFData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o
fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCELData.cpp -o
fusion/calvin_files/fusion/src/FusionCELData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionProbeSetResults.cpp -o
fusion/calvin_files/fusion/src/FusionProbeSetResults.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o
fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o
fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPLegacyData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o
fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPTilingData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPTilingData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPGenericData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPGenericData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o
fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parameter/src/ParameterNameValueType.cpp -o
fusion/calvin_files/parameter/src/ParameterNameValueType.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CDFFileReader.cpp -o
fusion/calvin_files/parsers/src/CDFFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CelFileReader.cpp -o
fusion/calvin_files/parsers/src/CelFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CHPFileReader.cpp -o
fusion/calvin_files/parsers/src/CHPFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o
fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CHPTilingFileReader.cpp -o
fusion/calvin_files/parsers/src/CHPTilingFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o
fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o
fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o
fusion/calvin_files/parsers/src/DataGroupHeaderReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/DataGroupReader.cpp -o
fusion/calvin_files/parsers/src/DataGroupReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/DataSetHeaderReader.cpp -o
fusion/calvin_files/parsers/src/DataSetHeaderReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/DataSetReader.cpp -o
fusion/calvin_files/parsers/src/DataSetReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/FileHeaderReader.cpp -o
fusion/calvin_files/parsers/src/FileHeaderReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/FileInput.cpp -o
fusion/calvin_files/parsers/src/FileInput.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o
fusion/calvin_files/parsers/src/GenericDataHeaderReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/parsers/src/GenericFileReader.cpp -o
fusion/calvin_files/parsers/src/GenericFileReader.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/utils/src/AffymetrixGuid.cpp -o
fusion/calvin_files/utils/src/AffymetrixGuid.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/DateTime.cpp
-o fusion/calvin_files/utils/src/DateTime.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/utils/src/FileUtils.cpp -o fusion/calvin_files/utils/src/FileUtils.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c
fusion/calvin_files/utils/src/StringUtils.cpp -o
fusion/calvin_files/utils/src/StringUtils.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/checksum.cpp
-o fusion/calvin_files/utils/src/checksum.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/BPMAPFileData.cpp -o
fusion/file/BPMAPFileData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/BPMAPFileWriter.cpp -o
fusion/file/BPMAPFileWriter.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/CDFFileData.cpp -o
fusion/file/CDFFileData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/CELFileData.cpp -o
fusion/file/CELFileData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
fusion/file/CELFileData.cpp: In member function ‘float
affxcel::CCELFileData::GetIntensity(int)’:
fusion/file/CELFileData.cpp:2409:41: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2409 | fIntensity=MmGetFloat_I(&m_pEntries[index].Intensity);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2414:41: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2414 | fIntensity=MmGetFloat_I(&(m_pEntries[index].Intensity));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2419:42: warning: taking address of packed member
of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer
value [-Waddress-of-packed-member]
2419 |
fIntensity=MmGetUInt16_N(&(m_pTransciptomeEntries[index].Intensity));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp: In member function ‘int
affxcel::CCELFileData::GetIntensities(int, std::vector<float>&)’:
fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2445 | intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2451 | intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member
of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer
value [-Waddress-of-packed-member]
2457 |
intensities[idx]=MmGetUInt16_N(&m_pTransciptomeEntries[idx].Intensity);
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp: In member function ‘float
affxcel::CCELFileData::GetStdv(int)’:
fusion/file/CELFileData.cpp:2506:37: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2506 | fStdev=MmGetFloat_I(&m_pEntries[index].Stdv);
| ^~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2509:37: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2509 | fStdev=MmGetFloat_I(&(m_pEntries[index].Stdv));
| ^~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2512:38: warning: taking address of packed member
of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer
value [-Waddress-of-packed-member]
2512 |
fStdev=MmGetUInt16_N(&(m_pTransciptomeEntries[index].Stdv));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp: In member function ‘short int
affxcel::CCELFileData::GetPixels(int)’:
fusion/file/CELFileData.cpp:2551:38: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2551 | sPixels=MmGetInt16_I(&m_pEntries[index].Pixels);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:2554:38: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
2554 | sPixels=MmGetInt16_I(&m_pEntries[index].Pixels);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp: In member function ‘void
affxcel::CCELFileData::SetIntensity(int, float)’:
fusion/file/CELFileData.cpp:3194:30: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
3194 | MmSetFloat_I(&m_pEntries[index].Intensity,intensity);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:3199:30: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
3199 | MmSetFloat_I(&m_pEntries[index].Intensity,intensity);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:3204:31: warning: taking address of packed member
of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer
value [-Waddress-of-packed-member]
3204 |
MmSetUInt16_N(&m_pTransciptomeEntries[index].Intensity,s);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp: In member function ‘void
affxcel::CCELFileData::SetStdv(int, float)’:
fusion/file/CELFileData.cpp:3251:31: warning: taking address of packed member
of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer
value [-Waddress-of-packed-member]
3251 | MmSetUInt16_N(&m_pTransciptomeEntries[index].Stdv,s);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp:3255:30: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
3255 | MmSetFloat_I(&m_pEntries[index].Stdv,stdev);
| ^~~~~~~~~~~~~~~~~~~~~~~
fusion/file/CELFileData.cpp: In member function ‘void
affxcel::CCELFileData::SetPixels(int, short int)’:
fusion/file/CELFileData.cpp:3294:42: warning: taking address of packed member
of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value
[-Waddress-of-packed-member]
3294 |
MmSetUInt16_I((uint16_t*)&m_pEntries[index].Pixels,(uint16_t)pixels);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/CHPFileData.cpp -o
fusion/file/CHPFileData.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/FileIO.cpp -o
fusion/file/FileIO.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/FileWriter.cpp -o
fusion/file/FileWriter.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/TsvFile/ClfFile.cpp -o
fusion/file/TsvFile/ClfFile.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/TsvFile/PgfFile.cpp -o
fusion/file/TsvFile/PgfFile.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/file/TsvFile/TsvFile.cpp -o
fusion/file/TsvFile/TsvFile.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/AffxByteArray.cpp -o
fusion/util/AffxByteArray.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/AffxConv.cpp -o
fusion/util/AffxConv.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/MsgStream.cpp -o
fusion/util/MsgStream.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/Util.cpp -o fusion/util/Util.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/Err.cpp -o fusion/util/Err.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/Fs.cpp -o fusion/util/Fs.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/Verbose.cpp -o
fusion/util/Verbose.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/RowFile.cpp -o
fusion/util/RowFile.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/TableFile.cpp -o
fusion/util/TableFile.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c fusion/util/Convert.cpp -o
fusion/util/Convert.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c R_affx_cel_parser.cpp -o
R_affx_cel_parser.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I.
-Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src
-Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src
-Ifusion/calvin_files/fusion/src/GCOSAdapter
-Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src
-Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src
-Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src
-Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile
-Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -Wno-sign-compare -O0 -c R_affx_cdf_parser.cpp -o
R_affx_cdf_parser.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
R_affx_cdf_parser.cpp: In function ‘SEXPREC* R_affx_get_cdf_cell_indices(SEXP,
SEXP, SEXP)’:
R_affx_cdf_parser.cpp:1099:17: error: format not a string literal and no format
arguments [-Werror=format-security]
1099 | error(s);
| ^
R_affx_cdf_parser.cpp: In function ‘SEXPREC* R_affx_get_cdf_units(SEXP, SEXP,
SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
R_affx_cdf_parser.cpp:1357:17: error: format not a string literal and no format
arguments [-Werror=format-security]
1357 | error(s);
| ^
R_affx_cdf_parser.cpp: In function ‘SEXPREC* R_affx_get_cdf_unit_names(SEXP,
SEXP, SEXP)’:
R_affx_cdf_parser.cpp:1730:17: error: format not a string literal and no format
arguments [-Werror=format-security]
1730 | error(s);
| ^
cc1plus: some warnings being treated as errors
make[2]: *** [Makevars:5: R_affx_cdf_parser.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘affxparser’
* removing
‘/<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library/affxparser’
dh_auto_install: error: R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-bioc-affxparser/usr/lib/R/site-library --clean .
"--built-timestamp='Wed, 29 Nov 2023 16:03:10 +0100'" returned exit code 1
make[1]: *** [debian/rules:7: override_dh_auto_install] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large from AWS, using sbuild and a
reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
