[Bioc-devel] Fwd: Package "SingleCellSignalR" failing on Bioconductor devel
Vincent Carey
@tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Sat Nov 26 12:35:37 CET 2022
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
> github: jorainer
> twitter: jo_rainer
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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