| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:37:45 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 813/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| geneXtendeR 1.29.0 (landing page) Bohdan Khomtchouk
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | TIMEOUT | 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: 1.29.0 |
| Command: rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.29.0.tar.gz |
| StartedAt: 2024-03-28 08:45:21 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 08:46:33 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 71.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: geneXtendeR_1.29.0.zip |
| PackageFileSize: 8.406 MiB |
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### Running command:
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### rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.29.0.tar.gz
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* installing *source* package 'geneXtendeR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int' [-Wformat=]
159 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %lld
annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
191 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %lld
annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
199 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %lld
annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
208 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %lld
annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
228 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %lld
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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;
| ^~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int' [-Wformat=]
202 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long long unsigned int
| %lld
gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/meat/geneXtendeR.buildbin-libdir/00LOCK-geneXtendeR/00new/geneXtendeR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'geneXtendeR' as geneXtendeR_1.29.0.zip
* DONE (geneXtendeR)