| 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 11:36:30 -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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL geneXtendeR |
| StartedAt: 2024-03-27 15:36:28 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:37:17 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 49.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL geneXtendeR
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
| ^~~~~~~~~~
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-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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-3.19-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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)