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.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
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