Bohdan Khomtchouk
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/geneXtendeR |
| git_branch: devel |
| git_last_commit: 05a7f4c |
| git_last_commit_date: 2024-10-29 10:14:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 807/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| geneXtendeR 1.33.0 (landing page) Bohdan Khomtchouk
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the geneXtendeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geneXtendeR.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. |
| Package: geneXtendeR |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL geneXtendeR |
| StartedAt: 2025-01-24 15:37:52 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 15:38:39 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 46.9 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘geneXtendeR’ ...
** this is package ‘geneXtendeR’ version ‘1.33.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:159:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
159 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:191:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
191 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:199:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
199 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:208:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
208 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:228:83: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
228 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:106:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
106 | fgets(varstr, 50000, varfp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
annotate.c:116:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
116 | fgets(vcfstr, 10000, vcffp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c extract_number.c -o extract_number.o
extract_number.c: In function ‘extractnumber’:
extract_number.c:98:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
98 | fgets(varstr, 50000, varfp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_number.c:108:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
108 | fgets(vcfstr, 10000, vcffp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c extract_peaks.c -o extract_peaks.o
extract_peaks.c: In function ‘extractpeaks’:
extract_peaks.c:202:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
202 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
107 | fgets(varstr, 50000, varfp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
117 | fgets(vcfstr, 10000, vcffp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-geneXtendeR/00new/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (geneXtendeR)