Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 805/2274 | 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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: geneXtendeR |
Version: 1.33.0 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL geneXtendeR |
StartedAt: 2024-12-23 20:07:00 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:08:02 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 62.0 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘geneXtendeR’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c extract_number.c -o extract_number.o extract_number.c: In function ‘extractnumber’: extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable] 72 | long n_1; | ^~~ extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable] 66 | long j_1; | ^~~ extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable] 54 | char * pvcfcol5_5; | ^~~~~~~~~~ extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable] 53 | char * pvcfcol4_4; | ^~~~~~~~~~ extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable] 52 | char * pvcfcol3_3; | ^~~~~~~~~~ extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable] 51 | char * pvcfcol2_2; | ^~~~~~~~~~ extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable] 50 | char * pvcfcol1_1; | ^~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-geneXtendeR/00new/geneXtendeR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (geneXtendeR)