Julius Muller
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/TransView |
| git_branch: RELEASE_3_20 |
| git_last_commit: 59648ff |
| git_last_commit_date: 2024-10-29 09:43:11 -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 12:08 -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 2185/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TransView 1.50.0 (landing page) Julius Muller
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
| 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 TransView package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.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: TransView |
| Version: 1.50.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL TransView |
| StartedAt: 2024-11-19 20:41:04 -0000 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 20:41:30 -0000 (Tue, 19 Nov 2024) |
| EllapsedTime: 26.2 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL TransView
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘TransView’ ...
** 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 -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_TransView.c -o R_init_TransView.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c bin_density.c -o bin_density.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c construct_dc.c -o construct_dc.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include/htslib/hts.h:36,
from /home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include/htslib/sam.h:33,
from /home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include/samtools-1.7-compat.h:5,
from parse_sam.h:4,
from construct_dc.c:23:
/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include/htslib/hts_log.h:76:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
76 | HTS_FORMAT(HTS_PRINTF_FMT, 3, 4);
| ^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c parse_sam.c -o parse_sam.o
parse_sam.c: In function 'quality_check':
parse_sam.c:161:75: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long int'} [-Wformat=]
161 | warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
| ~^ ~~~~~~~~~~~~~~~~~~~~~
| | |
| int hts_pos_t {aka long int}
| %ld
parse_sam.c:161:103: warning: format '%d' expects argument of type 'int', but argument 4 has type 'uint32_t *' {aka 'unsigned int *'} [-Wformat=]
161 | warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
| ~^
| |
| int
| %ls
parse_sam.c: In function 'print_readinfo':
parse_sam.c:202:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long int'} [-Wformat=]
202 | printf("Pos %d\n",current_read->core.pos);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| int hts_pos_t {aka long int}
| %ld
parse_sam.c:203:33: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long int'} [-Wformat=]
203 | printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int hts_pos_t {aka long int}
| %ld
parse_sam.c: In function 'seq_density':
parse_sam.c:314:61: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long int'} [-Wformat=]
314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
| ~^
| |
| int
| %ld
315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| hts_pos_t {aka long int}
parse_sam.c:314:94: warning: format '%d' expects argument of type 'int', but argument 6 has type 'hts_pos_t' {aka 'long int'} [-Wformat=]
314 | warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
| ~^
| |
| int
| %ld
315 | BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
316 | current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| hts_pos_t {aka long int}
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:184:33: warning: 'slicep' may be used uninitialized [-Wmaybe-uninitialized]
184 | expand(slicep,new_vecp,rebuildc,wsize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
slice_dc.c:101:22: note: 'slicep' was declared here
101 | int *slicep= INTEGER_POINTER(slice);
| ^~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c visuals.c -o visuals.o
gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /home/biocbuild/R/R-4.4.1/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-TransView/00new/TransView/libs
** R
** 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 (TransView)