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.coli...@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@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.coli...@inserm.fr > Date: Thu, 17 Nov 2022 08:14:12 +0000 > From: Johannes Rainer <johannes.rai...@eurac.edu> > To: Jacques Colinge <jacques.coli...@inserm.fr> > CC: bioconductorcoret...@gmail.com <bioconductorcoret...@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@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.rai...@eurac.edu > <mailto:email%3ajohannes.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 > > > The information in this e-mail is intended only for th...{{dropped:30}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel