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This page was generated on 2025-12-11 13:10 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" | 926 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 61/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| csaw 1.45.0 (landing page) Aaron Lun
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||
|
To the developers/maintainers of the csaw package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: csaw |
| Version: 1.45.0 |
| Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data csaw |
| StartedAt: 2025-12-11 12:30:14 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 12:30:44 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 29.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data csaw
###
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* checking for file ‘csaw/DESCRIPTION’ ... OK
* preparing ‘csaw’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
-----------------------------------
* installing *source* package ‘csaw’ ...
** this is package ‘csaw’ version ‘1.45.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c annotator.cpp -o annotator.o
annotator.cpp: In function ‘SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
annotator.cpp:47:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
47 | while (counter < nolaps && query[counter]==curreg) {
| ~~~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c bam_utils.cpp -o bam_utils.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function ‘SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)’:
best_in_cluster.cpp:11:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
11 | if (nwin!=clustids.size() || nwin!=winweight.size()) {
| ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:42: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
11 | if (nwin!=clustids.size() || nwin!=winweight.size()) {
| ~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c check_bimodality.cpp -o check_bimodality.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c correlate_reads.cpp -o correlate_reads.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c find_maxima.cpp -o find_maxima.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c get_profile.cpp -o get_profile.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c get_rle_counts.cpp -o get_rle_counts.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c intersector.cpp -o intersector.o
intersector.cpp: In constructor ‘intersector::intersector(SEXP, SEXP)’:
intersector.cpp:8:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
8 | if (N!=elements.size()) {
| ~^~~~~~~~~~~~~~~~~
intersector.cpp:32:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
32 | if (current < 0 || current >= nelements) {
| ~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c merge_windows.cpp -o merge_windows.o
merge_windows.cpp:127:1: fatal error: error writing to /tmp/ccYZdHdt.s: No space left on device
127 | }
| ^
compilation terminated.
make: *** [/home/rapidbuild/bbs-3.23-bioc-rapid/R/etc/Makeconf:209: merge_windows.o] Error 1
ERROR: compilation failed for package ‘csaw’
* removing ‘/tmp/RtmprIHhxw/Rinst36ddd07ac53953/csaw’
-----------------------------------
ERROR: package installation failed