Aaron Lun
| Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/csaw |
| git_branch: devel |
| git_last_commit: 11222da |
| git_last_commit_date: 2024-04-30 10:39:51 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-01 11:44 -0400 (Mon, 01 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4409 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
| 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 458/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| csaw 1.39.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the csaw package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/csaw.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: csaw |
| Version: 1.39.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL csaw |
| StartedAt: 2024-06-30 19:24:56 -0000 (Sun, 30 Jun 2024) |
| EndedAt: 2024-06-30 19:27:27 -0000 (Sun, 30 Jun 2024) |
| EllapsedTime: 150.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL csaw
###
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* installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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:11:10: 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]
11 | if (nwin!=clustids.size() || nwin!=winweight.size()) {
| ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:35: 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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/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/biocbuild/R/R-4.4.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.4.0/lib -lR
installing to /home/biocbuild/R/R-4.4.0/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)