Hi Jasmin,
that looks like a conda bug - I don't get that error message. I'd try a
simple
conda install zlib
Also, I suggest that we deal with this off-list to reduce mailing list
traffic.
Cheers,
p.
On 07/09/19 15:58, Jasmin wrote:
Hi Paolo,
thank you for your help! I'm getting closer :D
Now I get the error:
"
-- Could NOT find ZLIB (missing: ZLIB_LIBRARY) (found version "1.2.11")
-- coordgen include dir set as
/home/User/programs/rdkit/External/CoordGen
-- coordgen libraries set as 'coordgen_LIBRARIES-NOTFOUND'
-- coordgen templates file set as 'coordgen_TEMPLATE_FILE-NOTFOUND'
-- Could NOT find coordgen (missing: coordgen_LIBRARIES
coordgen_TEMPLATE_FILE)
-- Found coordgenlibs source in
/home/User/programs/rdkit/External/CoordGen/coordgen
-- Could NOT find ZLIB (missing: ZLIB_LIBRARY) (found version "1.2.11")
"
Unfortunately, "conda install -c anaconda zlib" produces
" An unexpected error has occurred. Conda has prepared the above
report. "
which reads:
"
environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_ADDR2LINE=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
addr2line
CONDA_BACKUP_AR=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-ar
CONDA_BACKUP_AS=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-as
CONDA_BACKUP_CC=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe
CONDA_BACKUP_CPP=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-cpp
CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
CONDA_BACKUP_CXX=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++
CONDA_BACKUP_CXXFILT=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-
gnu-c++filt
CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17
-fmessage-length=0
-march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe
CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra
-fvar-tracking-assignments
-ffunction-sections -pipe
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17
-fmessage-length=0
-march=nocona -mtune=haswell
-ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra
-fvar-tracking-assignments
-ffunction-sections -pipe
CONDA_BACKUP_ELFEDIT=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
elfedit
CONDA_BACKUP_GCC=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_BACKUP_GCC_AR=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
ar
CONDA_BACKUP_GCC_NM=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
nm
CONDA_BACKUP_GCC_RANLIB=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
ranlib
CONDA_BACKUP_GPROF=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
gprof
CONDA_BACKUP_GXX=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-g++
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
CONDA_BACKUP_LD=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed
-Wl,-z,relro -Wl,-z,now -Wl,
--disable-new-dtags -Wl,--gc-sections
CONDA_BACKUP_LD_GOLD=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
ld.gold
CONDA_BACKUP_NM=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_BACKUP_OBJCOPY=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
objcopy
CONDA_BACKUP_OBJDUMP=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
objdump
CONDA_BACKUP_RANLIB=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
ranlib
CONDA_BACKUP_READELF=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
readelf
CONDA_BACKUP_SIZE=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-size
CONDA_BACKUP_STRINGS=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
strings
CONDA_BACKUP_STRIP=/home/User/programs/Miniconda3/bin/x86_64-conda_cos6-linux-gnu-
strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
CONDA_DEFAULT_ENV=dev_env
CONDA_EXE=/home/User/programs/Miniconda3/bin/conda
CONDA_PREFIX=/home/User/programs/Miniconda3/envs/dev_env
CONDA_PREFIX_1=/home/User/programs/Miniconda3
CONDA_PROMPT_MODIFIER=
CONDA_PYTHON_EXE=/home/User/programs/Miniconda3/bin/python
CONDA_ROOT=/home/User/programs/Miniconda3
CONDA_SHLVL=2
PATH=/home/User/programs/Miniconda3/bin:/home/User/programs/Miniconda
3/envs/dev_env/bin:/home/User/programs/Miniconda3/condabin:/usr/loc
al/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/l
ocal/games:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
ftp_proxy=<set>
http_proxy=<set>
https_proxy=<set>
active environment : dev_env
active env location : /home/User/programs/Miniconda3/envs/dev_env
shell level : 2
user config file : /home/User/.condarc
populated config files : /home/User/.condarc
conda version : 4.7.5
conda-build version : not installed
python version : 3.7.3.final.0
virtual packages :
base environment : /home/User/programs/Miniconda3 (writable)
channel URLs : https://conda.anaconda.org/anaconda/linux-64
https://conda.anaconda.org/anaconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/User/programs/Miniconda3/pkgs
/home/User/.conda/pkgs
envs directories : /home/User/programs/Miniconda3/envs
/home/User/.conda/envs
platform : linux-64
user-agent : conda/4.7.5 requests/2.21.0 CPython/3.7.3
Linux/4.18.0-1024-azure ubuntu/18.04.2 glibc/2.27
UID:GID : 1002:1003
netrc file : None
offline mode : False
"
(I replaced my Username with "User".)
Best,
Jasmin
Am 09.07.2019 13:30 schrieb Paolo Tosco:
Hi Jasmin,
after you have activated your environment it should be sufficient to
run the command
conda install boost
and then build the RDKit as you were doing previously. cmake should
now pick the conda Boost instead of system Boost.
Cheers,
p.
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