| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| 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 33/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| csaw 1.36.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
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: 1.36.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL csaw |
| StartedAt: 2024-03-08 15:31:46 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 15:33:19 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 92.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL csaw
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* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam_utils.cpp -o bam_utils.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_maxima.cpp -o find_maxima.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c get_profile.cpp -o get_profile.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c merge_windows.cpp -o merge_windows.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c pair_reads.cpp -o pair_reads.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c single_reads.cpp -o single_reads.o
g++ -std=gnu++11 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/zlibbioc/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_profile.o get_rle_counts.o init.o intersector.o merge_windows.o pair_reads.o single_reads.o utils.o /home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/R/site-library/00LOCK-csaw/00new/csaw/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (csaw)