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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2185/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.50.0  (landing page)
Julius Muller
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: RELEASE_3_20
git_last_commit: 21d33cd
git_last_commit_date: 2024-12-12 03:54:15 -0500 (Thu, 12 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

INSTALL results for TransView on merida1

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.

raw results


Summary

Package: TransView
Version: 1.50.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TransView
StartedAt: 2024-12-19 15:22:21 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 15:22:58 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 37.1 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TransView
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TransView’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_TransView.c -o R_init_TransView.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bin_density.c -o bin_density.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c construct_dc.c -o construct_dc.o
In file included from construct_dc.c:23:
In file included from ./parse_sam.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/sam.h:33:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts.h:36:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts_log.h:76:1: warning: '__format__' attribute argument not supported: Rprintf [-Wignored-attributes]
HTS_FORMAT(HTS_PRINTF_FMT, 3, 4);
^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/htslib/hts_defs.h:101:53: note: expanded from macro 'HTS_FORMAT'
#define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first)))
                                                    ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c parse_sam.c -o parse_sam.o
parse_sam.c:161:88: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat]
                        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));
                                                                         ~~                                 ^~~~~~~~~~~~~~~~~~~~~
                                                                         %lld
parse_sam.c:161:133: warning: format specifies type 'int' but the argument has type 'uint32_t *' (aka 'unsigned int *') [-Wformat]
                        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));
                                                                                                     ~~                                                  ^~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include/samtools-1.7-compat.h:23:23: note: expanded from macro 'bam1_cigar'
#define bam1_cigar(b) (bam_get_cigar((b)))
                      ^~~~~~~~~~~~~~~~~~~~
parse_sam.c:202:20: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat]
        printf("Pos %d\n",current_read->core.pos);
                    ~~    ^~~~~~~~~~~~~~~~~~~~~~
                    %lld
parse_sam.c:203:47: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
        printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos);
                               ~~                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                               %lld
parse_sam.c:315:18: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat]
                                        BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
                                                    ^~~~~~~~~~~~~~~~~~~~~~
parse_sam.c:316:6: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
                                        current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c slice_dc.c -o slice_dc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c visuals.c -o visuals.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)