Andreas Mitterecker
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/hapFabia |
| git_branch: RELEASE_3_20 |
| git_last_commit: 47dfa0f |
| git_last_commit_date: 2024-10-29 09:42:32 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 933/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hapFabia 1.48.0 (landing page) Andreas Mitterecker
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the hapFabia package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hapFabia.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: hapFabia |
| Version: 1.48.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL hapFabia |
| StartedAt: 2024-11-19 20:27:44 -0000 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 20:28:13 -0000 (Tue, 19 Nov 2024) |
| EllapsedTime: 28.2 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL hapFabia
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘hapFabia’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c interfaceR.c -o interfaceR.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c vcftoFABIAB.c -o vcftoFABIAB.o
vcftoFABIAB.c: In function 'getdelimS':
vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
50 | if (ch == EOF)
| ^~
vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
54 | while (idx > *linebufsz - 2) {
| ^~~~~
vcftoFABIAB.c: In function 'vcftoFABIAB':
vcftoFABIAB.c:352:19: warning: '__builtin_strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
352 | strncat(minor[j],Iminor,190);
| ^~~~~~~
vcftoFABIAB.c:382:19: warning: '__builtin_strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
382 | strncat(info[j],Iinfo,190);
| ^~~~~~~
vcftoFABIAB.c:394:19: warning: '__builtin_strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
394 | strncat(format[j],Iformat,19);
| ^~~~~~~
vcftoFABIAB.c:362:19: warning: '__builtin_strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
362 | strncat(qual[j],Iqual,19);
| ^~~~~~~
vcftoFABIAB.c:372:19: warning: '__builtin_strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
372 | strncat(filter[j],Ifilter,19);
| ^~~~~~~
vcftoFABIAB.c:332:19: warning: '__builtin_strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
332 | strncat(snpName[j],IsnpName,49);
| ^~~~~~~
vcftoFABIAB.c:342:19: warning: '__builtin_strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
342 | strncat(major[j],Imajor,190);
| ^~~~~~~
vcftoFABIAB.c:250:21: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
250 | snpName[0] = calloc((long) 50*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from vcftoFABIAB.c:2:
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
vcftoFABIAB.c:258:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
258 | filter[0] = calloc((long) 20*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
vcftoFABIAB.c:266:18: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
266 | qual[0] = calloc((long) 20*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
vcftoFABIAB.c:281:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
281 | format[0] = calloc((long) 20*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/R/R-4.4.1/lib -lR
gcc -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall
gcc -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall
gcc ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 -Wall
gcc -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall
vcftoFABIAB.c: In function 'getdelimS':
vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
50 | if (ch == EOF)
| ^~
vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
54 | while (idx > *linebufsz - 2) {
| ^~~~~
vcftoFABIAB.c: In function 'vcftoFABIAB':
vcftoFABIAB.c:352:19: warning: '__builtin_strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
352 | strncat(minor[j],Iminor,190);
| ^~~~~~~
vcftoFABIAB.c:382:19: warning: '__builtin_strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
382 | strncat(info[j],Iinfo,190);
| ^~~~~~~
vcftoFABIAB.c:394:19: warning: '__builtin_strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
394 | strncat(format[j],Iformat,19);
| ^~~~~~~
vcftoFABIAB.c:362:19: warning: '__builtin_strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
362 | strncat(qual[j],Iqual,19);
| ^~~~~~~
vcftoFABIAB.c:372:19: warning: '__builtin_strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
372 | strncat(filter[j],Ifilter,19);
| ^~~~~~~
vcftoFABIAB.c:332:19: warning: '__builtin_strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
332 | strncat(snpName[j],IsnpName,49);
| ^~~~~~~
vcftoFABIAB.c:342:19: warning: '__builtin_strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
342 | strncat(major[j],Imajor,190);
| ^~~~~~~
vcftoFABIAB.c:250:21: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
250 | snpName[0] = calloc((long) 50*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from vcftoFABIAB.c:2:
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
vcftoFABIAB.c:258:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
258 | filter[0] = calloc((long) 20*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
vcftoFABIAB.c:266:18: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
266 | qual[0] = calloc((long) 20*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
vcftoFABIAB.c:281:20: warning: argument 1 range [9223372036854775808, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
281 | format[0] = calloc((long) 20*snps, sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-hapFabia/00new/hapFabia/libs
** R
** data
** 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 (hapFabia)