[Bioc-devel] Fwd: Package "SingleCellSignalR" failing on Bioconductor devel
Jacques Colinge
j@cque@@co||nge @end|ng |rom umontpe|||er@|r
Thu Dec 8 14:44:24 CET 2022
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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