Message-ID: <dfd91e59-3eaa-89da-0e79-ba9ecb5e51fe@umontpellier.fr>
Date: 2022-12-08T13:44:24Z
From: Jacques Colinge
Subject: [Bioc-devel] Fwd: Package "SingleCellSignalR" failing on Bioconductor devel
In-Reply-To: <CAANT7+UiD=0cXECYi2+mGyx9BvZpzVtWtH2DWQu0BSL5eerjoQ@mail.gmail.com>
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 at 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 at 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
> ?????????????????????????????????????????????????????????????????????????????????????????????????????????
> ? 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 at inserm.fr
> Date:? ?Thu, 17 Nov 2022 08:14:12 +0000
> From:? ?Johannes Rainer <johannes.rainer at eurac.edu>
> To:? ? ?Jacques Colinge <jacques.colinge at inserm.fr>
> CC: bioconductorcoreteam at gmail.com <bioconductorcoreteam at 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 at 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 at eurac.edu
> <mailto:email%3Ajohannes.rainer at eurac.edu>
> github: jorainer
> twitter: jo_rainer
>
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