[Bioc-devel] Fwd: Package "SingleCellSignalR" failing on Bioconductor devel
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Dec 8 16:55:31 CET 2022
FWIW the compilation error for SIMLR looks like a real error to me, not
a warning-induced one:
tsne.cpp:883:11: error: too few arguments to function ‘void dgemm_(...
It seems to be caused by a change in R-devel. We see it on all platforms
on the daily builds for BioC 3.17 and I also get it on my laptop.
Anybody using a recent R-devel should be able to reproduce it.
Cheers,
H.
On 08/12/2022 05:44, Jacques Colinge wrote:
> Dear Vincent,
>
> Thank you very much for this information. The problem should be fixed
> now, build and check are successful in R develeopment version. I have
> just pushed my fixes onto bioconductor github.
>
> Best regards,
> Jacques
>
> On 26.11.2022 12:35, Vincent Carey wrote:
>> When testing on the devel branch at this time, you must use R-devel (R
>> 4.3). See
>> https://contributions.bioconductor.org/use-devel.html#use-devel
>>
>> For SingleCellSignalR, the dependence on SIMLR seems problematic.
>> SIMLR is in an error state on the devel branch. One
>> could see that even in the release branch, SIMLR includes some code
>> that is risky:
>>
>> * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
>> * installing *source* package ‘SIMLR’ ...
>> ** using staged installation
>> ** libs
>> g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
>> g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rtsne.cpp -o Rtsne.o
>> gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c package_init.c -o package_init.o
>> gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c projsplx_R.c -o projsplx_R.o
>> g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c sptree.cpp -o sptree.o
>> g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c tsne.cpp -o tsne.o
>> tsne.cpp: In member function ‘bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)’:
>> tsne.cpp:967:48: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
>> 967 | if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
>> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
>> but it passed on the release branch. On the devel branch SIMLR fails. The sources for
>> SIMLR don't appear to have changed since 2017 (reading git log). So this seems like a situation
>> in which a package that has not changed since release fails in devel because
>> the tolerance of the build system for compiler-flagged warning events has been reduced.
>> The developers of SIMLR will need to fix this, or you will have to eliminate the dependence on
>> SIMLR from your package. Your favorable results for CMD check arise from a) not working
>> in the devel branch and b) having a version of SIMLR that built under out-of-date warning
>> tolerance compiler settings. Let us know if there are further questions.
>>
>> On Sat, Nov 26, 2022 at 6:15 AM Jacques Colinge
>> <jacques.colinge using umontpellier.fr> wrote:
>>
>> Dear Johannes,
>> Dear Bioc Developers,
>>
>> I am not sure I get the problem. I am currently running R 4.2.1
>> and if I
>> do a devtools::check() and a devtools::build() I have no error
>> (just one
>> warning), see below both outputs.
>>
>> Do you need me to install R development version and redo those tests
>> because with this new versions some errors occur?
>>
>> Thanks for your answer.
>> Best regards,
>> Jacques
>>
>> ------- check() output -------------------------
>>
>> jcolinge using osboxes:~/SingleCellSignalR$ R
>>
>> R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
>> Copyright (C) 2022 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> > library(devtools)
>> Loading required package: usethis
>> > devtools::check()
>> ══ Documenting
>> ═════════════════════════════════════════════════════════════════════════════════════════════════════════
>> ℹ Installed roxygen2 version (7.2.1) doesn't match required (7.0.2)
>> ✖ `check()` will not re-document this package
>> ══ Building
>> ════════════════════════════════════════════════════════════════════════════════════════════════════════════
>> Setting env vars:
>> • CFLAGS : -Wall -pedantic -fdiagnostics-color=always
>> • CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
>> • CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
>> • CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
>> • CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
>> • CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
>> ✔ checking for file
>> ‘/home/jcolinge/SingleCellSignalR/DESCRIPTION’ ...
>> ─ preparing ‘SingleCellSignalR’:
>> ✔ checking DESCRIPTION meta-information ...
>> ─ installing the package to build vignettes
>>
>> ✔ creating vignettes (50.9s)
>> ─ checking for LF line-endings in source and make files and shell
>> scripts
>> ─ checking for empty or unneeded directories
>> ─ building ‘SingleCellSignalR_0.99.24.tar.gz’
>>
>> ══ Checking
>> ════════════════════════════════════════════════════════════════════════════════════════════════════════════
>> Setting env vars:
>> • _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
>> • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
>> • _R_CHECK_CRAN_INCOMING_ : FALSE
>> • _R_CHECK_FORCE_SUGGESTS_ : FALSE
>> • NOT_CRAN : true
>> ── R CMD check
>> ─────────────────────────────────────────────────────────────────────────────────────────────────────────
>> ─ using log directory ‘/tmp/RtmpJDbnZF/SingleCellSignalR.Rcheck’
>> ─ using R version 4.2.1 (2022-06-23)
>> ─ using platform: x86_64-pc-linux-gnu (64-bit)
>> ─ using session charset: UTF-8
>> ─ using options ‘--no-manual --as-cran’
>> ✔ checking for file ‘SingleCellSignalR/DESCRIPTION’
>> ─ this is package ‘SingleCellSignalR’ version ‘0.99.24’
>> ─ package encoding: UTF-8
>> ✔ checking package namespace information
>> ✔ checking package dependencies (3s)
>> ✔ checking if this is a source package
>> ✔ checking if there is a namespace
>> ✔ checking for executable files ...
>> ✔ checking for hidden files and directories
>> ✔ checking for portable file names
>> ✔ checking for sufficient/correct file permissions
>> ✔ checking whether package ‘SingleCellSignalR’ can be installed
>> (23.8s)
>> N checking installed package size ...
>> installed size is 6.6Mb
>> sub-directories of 1Mb or more:
>> data 5.9Mb
>> ✔ checking package directory
>> ✔ checking for future file timestamps ...
>> ✔ checking ‘build’ directory
>> ✔ checking DESCRIPTION meta-information ...
>> ✔ checking top-level files ...
>> ✔ checking for left-over files
>> ✔ checking index information ...
>> ✔ checking package subdirectories ...
>> ✔ checking R files for non-ASCII characters ...
>> ✔ checking R files for syntax errors ...
>> ✔ checking whether the package can be loaded (5.7s)
>> ✔ checking whether the package can be loaded with stated
>> dependencies
>> (5.3s)
>> ✔ checking whether the package can be unloaded cleanly (5.3s)
>> ✔ checking whether the namespace can be loaded with stated
>> dependencies
>> (5.4s)
>> ✔ checking whether the namespace can be unloaded cleanly (5.6s)
>> ✔ checking dependencies in R code (5.4s)
>> ✔ checking S3 generic/method consistency (7.5s)
>> ✔ checking replacement functions (5.4s)
>> ✔ checking foreign function calls (5.4s)
>> ✔ checking R code for possible problems (25.6s)
>> ✔ checking Rd files ... OK
>> ✔ checking Rd metadata ...
>> ✔ checking Rd line widths ...
>> ✔ checking Rd cross-references ... OK
>> ✔ checking for missing documentation entries (6.5s)
>> ✔ checking for code/documentation mismatches (18.5s)
>> ✔ checking Rd \usage sections (7.3s)
>> ✔ checking Rd contents ... OK
>> ✔ checking for unstated dependencies in examples ... OK
>> ✔ checking contents of ‘data’ directory (2.3s)
>> ✔ checking data for non-ASCII characters (2.7s)
>> W checking LazyData
>> LazyData DB of 5.9 MB without LazyDataCompression set
>> See §1.1.6 of 'Writing R Extensions'
>> ✔ checking data for ASCII and uncompressed saves ...
>> ✔ checking installed files from ‘inst/doc’ ...
>> ✔ checking files in ‘vignettes’ ... OK
>> ✔ checking examples (15s)
>> ✔ checking for unstated dependencies in vignettes ...
>> ✔ checking package vignettes in ‘inst/doc’ ... OK
>> ✔ checking re-building of vignette outputs (22.9s)
>> N checking for non-standard things in the check directory
>> Found the following files/directories:
>> ‘cell-classification’ ‘cluster-analysis’ ‘data’ ‘images’
>> ‘networks’
>> ✔ checking for detritus in the temp directory
>>
>> See
>> ‘/tmp/RtmpJDbnZF/SingleCellSignalR.Rcheck/00check.log’
>> for details.
>>
>>
>> ── R CMD check results
>> ──────────────────────────────────────────────────────────────────
>> SingleCellSignalR 0.99.24 ────
>> Duration: 3m 1.1s
>>
>> ❯ checking LazyData ... WARNING
>> LazyData DB of 5.9 MB without LazyDataCompression set
>> See §1.1.6 of 'Writing R Extensions'
>>
>> ❯ checking installed package size ... NOTE
>> installed size is 6.6Mb
>> sub-directories of 1Mb or more:
>> data 5.9Mb
>>
>> ❯ checking for non-standard things in the check directory ... NOTE
>> Found the following files/directories:
>> ‘cell-classification’ ‘cluster-analysis’ ‘data’ ‘images’
>> ‘networks’
>>
>> 0 errors ✔ | 1 warning ✖ | 2 notes ✖
>>
>>
>> --------------- build() output
>> --------------------------------------------------
>>
>> > devtools::build()
>> ✔ checking for file
>> ‘/home/jcolinge/SingleCellSignalR/DESCRIPTION’ ...
>> ─ preparing ‘SingleCellSignalR’:
>> ✔ checking DESCRIPTION meta-information ...
>> ─ installing the package to build vignettes
>> ✔ creating vignettes (44.8s)
>> ─ checking for LF line-endings in source and make files and shell
>> scripts
>> ─ checking for empty or unneeded directories
>> ─ building ‘SingleCellSignalR_0.99.24.tar.gz’
>>
>> [1] "/home/jcolinge/SingleCellSignalR_0.99.24.tar.gz"
>>
>>
>> -------- Forwarded Message --------
>> Subject: Package "SingleCellSignalR" failing on
>> Bioconductor devel
>> Resent-Date: Thu, 17 Nov 2022 09:14:15 +0100
>> Resent-From: jacques.colinge using inserm.fr
>> Date: Thu, 17 Nov 2022 08:14:12 +0000
>> From: Johannes Rainer <johannes.rainer using eurac.edu>
>> To: Jacques Colinge <jacques.colinge using inserm.fr>
>> CC: bioconductorcoreteam using gmail.com <bioconductorcoreteam using gmail.com>
>>
>>
>>
>> Hello Package Maintainer,
>>
>> The Bioconductor Team would like to notify you that your package
>> "SingleCellSignalR" is currently failing on the devel version of
>> Bioconductor. Please fix your package to R CMD build and R CMD
>> check 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 using r-project.org
>>
>> We appreciate your attention to this matter.
>>
>> Best Regtards,
>> Johannes
>>
>> --
>> Johannes Rainer, PhD
>>
>> Eurac Research
>> Institute for Biomedicine
>> Via A.-Volta 21, I-39100 Bolzano, Italy
>>
>> email:johannes.rainer using eurac.edu
>> <mailto:email%3Ajohannes.rainer using eurac.edu>
>> github: jorainer
>> twitter: jo_rainer
>>
>> [[alternative HTML version deleted]]
>>
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