Re: [Bioc-devel] Package "sigPathway" failing on Bioconductor devel
To whom it may concern: I am writing to request the sigPathway package to be deprecated at this time. It has been 16 years since I last made any significant changes to its codebase. I have changed careers and currently lack the knowledgebase or time to properly fix the build failure. Of note, for those who may be interested in fixing the package for future internal use, I suspect it is failing to compile on Bioconductor devel (3.17) because of changes made in R 4.2.x codebase: "USE_FC_LEN_T will become the default: this uses the correct prototypes for Fortran BLAS/LAPACK routines called from C/C++, and requires adjustment of most such calls � see �Writing R Extensions� �6.6.1. (This has been supported since R 3.6.2.)" (excerpt from https://cran.r-project.org/doc/manuals/r-release/NEWS.html) Best Regards, Weil Lai, MD From: Johannes Rainer Sent: Friday, December 2, 2022 4:13 AM To: Weil Lai Cc: bioconductorcoret...@gmail.com Subject: Package "sigPathway" failing on Bioconductor devel Dear Package Maintainer, this is a reminder to fix your package "sigPathway" that is still failing on Bioconductor devel (3.17). Please fix your package to R CMD build and R CMD check cleanly to avoid deprecation of your package. While devel is a place to experiment with new features, we expect packages to build and check cleanly in a reasonable time period and not stay broken for any extended period of time. If you are having trouble or have any further questions please do not hesitate to reach out to the developers mailing list at bioc-devel@r-project.org We appreciate your attention to this matter. Best Regards, Johannes -- Johannes Rainer, PhD Eurac Research Institute for Biomedicine Via A.-Volta 21, I-39100 Bolzano, Italy email: johannes.rai...@eurac.edu github: jorainer twitter: jo_rainer [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] error on R CMD check
Hi,
On 06/12/2022 21:01, Zhigang Li wrote:
Dear Bioconductor Developers,
Can you please help with an error message from R CMD check for the package IFAA?
The BioConductor platform produced the following error message when
running R CMD check
(http://bioconductor.org/checkResults/devel/bioc-LATEST/IFAA/nebbiolo1-checksrc.html):
"
BiocGenerics:::testPackage("IFAA")
Error in BiocGenerics:::testPackage("IFAA") :
unable to find unit tests, no subdir 'unitTests'
Execution halted
"
However, the error is very strange because the subdirectory
"unitTests" is there in the folder "inst". And we have previously
passed the test of the package thru the github webpage
(https://github.com/Bioconductor/Contributions/issues/2651). We have
also tested it on our own computer and it did not have this error.
Below is the output from our personal computer.
(base) quranwu@MacBook-Pro-4 test % R CMD check --library=./
--no-vignettes --timings IFAA_0.99.9.tar.gz
* using log directory ‘/Users/quranwu/Desktop/test/IFAA.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IFAA/DESCRIPTION’ ... OK
* this is package ‘IFAA’ version ‘0.99.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IFAA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
IFAA 12.723 0.146 72.684
MZILN 0.944 0.020 15.038
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
By any chance could it be because the IFAA package on CRAN got called
when running BiocGenerics:::testPackage("IFAA") on the BioConductor
platform? The IFAA package on CRAN indeed does not have the
subdirectory of "unitTests".
Probably. At the root of the problem is the fact that the IFAA package
on CRAN is at version 1.1.0 but was submitted to Bioconductor with
version 0.99.z. When a CRAN package is submitted to Bioconductor, it
doesn't make sense to reset the version to 0.99.z. More generally
speaking, package versions should **never** go down because this
introduces all kinds of problems.
For example, even if the IFAA package in Bioconductor somehow managed to
pass 'R CMD check' and propagate to the Bioconductor repos, users would
be unable to install it because BiocManager::install("IFAA") would pick
up the higher version. And even if a user was somehow able to install
it, it would be very quickly replaced with the CRAN version the next
time the user updates their packages (something users and developers
should do on a regular basis by calling BiocManager::install() with no
arguments).
What is happening exactly on the build machines with
BiocGenerics:::testPackage("IFAA") is a
[Bioc-devel] error on R CMD check
Dear Bioconductor Developers,
Can you please help with an error message from R CMD check for the package IFAA?
The BioConductor platform produced the following error message when
running R CMD check
(http://bioconductor.org/checkResults/devel/bioc-LATEST/IFAA/nebbiolo1-checksrc.html):
"
BiocGenerics:::testPackage("IFAA")
Error in BiocGenerics:::testPackage("IFAA") :
unable to find unit tests, no subdir 'unitTests'
Execution halted
"
However, the error is very strange because the subdirectory
"unitTests" is there in the folder "inst". And we have previously
passed the test of the package thru the github webpage
(https://github.com/Bioconductor/Contributions/issues/2651). We have
also tested it on our own computer and it did not have this error.
Below is the output from our personal computer.
(base) quranwu@MacBook-Pro-4 test % R CMD check --library=./
--no-vignettes --timings IFAA_0.99.9.tar.gz
* using log directory ‘/Users/quranwu/Desktop/test/IFAA.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IFAA/DESCRIPTION’ ... OK
* this is package ‘IFAA’ version ‘0.99.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IFAA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
IFAA 12.723 0.146 72.684
MZILN 0.944 0.020 15.038
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
By any chance could it be because the IFAA package on CRAN got called
when running BiocGenerics:::testPackage("IFAA") on the BioConductor
platform? The IFAA package on CRAN indeed does not have the
subdirectory of "unitTests".
Thanks,
Zhigang
https://sites.google.com/view/zlab
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