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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 2169/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.51.0  (landing page)
Julius Muller
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: devel
git_last_commit: 4ecba1b
git_last_commit_date: 2024-12-12 03:43:53 -0500 (Thu, 12 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


INSTALL results for TransView on nebbiolo1

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: 1.51.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL TransView
StartedAt: 2024-12-23 15:11:59 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 15:12:03 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 4.0 seconds
RetCode: 1
Status:   ERROR  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL TransView
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘TransView’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c R_init_TransView.c -o R_init_TransView.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c bin_density.c -o bin_density.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c construct_dc.c -o construct_dc.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include/htslib/hts.h:36,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include/htslib/sam.h:33,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include/samtools-1.7-compat.h:5,
                 from parse_sam.h:4,
                 from construct_dc.c:23:
/home/biocbuild/bbs-3.21-bioc/R/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);
      | ^~~~~~~~~~
construct_dc.c: In function ‘set_filter’:
construct_dc.c:58:37: warning: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
   58 |         ft->sequence_name = (char**)Calloc(flen,char*);
      |                                     ^~~~~~
      |                                     calloc
construct_dc.c:58:49: error: expected expression before ‘char’
   58 |         ft->sequence_name = (char**)Calloc(flen,char*);
      |                                                 ^~~~
construct_dc.c:59:46: error: expected expression before ‘int32_t’
   59 |         ft->values = (int32_t **)Calloc(flen,int32_t*);
      |                                              ^~~~~~~
construct_dc.c:60:51: error: expected expression before ‘int32_t’
   60 |         ft->value_length = (int32_t *)Calloc(flen,int32_t);
      |                                                   ^~~~~~~
construct_dc.c:65:84: error: expected expression before ‘char’
   65 |                 ft->sequence_name[j] = Calloc(strlen(CHAR(STRING_ELT(fnames, j))), char);
      |                                                                                    ^~~~
construct_dc.c: In function ‘destroy_filter’:
construct_dc.c:85:41: warning: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration]
   85 |                 if(ft->sequence_name[j])Free(ft->sequence_name[j]);
      |                                         ^~~~
      |                                         free
construct_dc.c: In function ‘write_density’:
construct_dc.c:172:55: error: expected expression before ‘uint32_t’
  172 |         proc_chrom=Calloc(bam_file->header->n_targets,uint32_t);
      |                                                       ^~~~~~~~
construct_dc.c:198:44: error: expected expression before ‘usersize’
  198 |                 cptr = Calloc(cs.max_pos+1,usersize);
      |                                            ^~~~~~~~
construct_dc.c:199:53: error: expected expression before ‘uint32_t’
  199 |                 lstart_ind=Calloc(cs.min_indexspace,uint32_t);
      |                                                     ^~~~~~~~
construct_dc.c:200:51: error: expected expression before ‘uint32_t’
  200 |                 lend_ind=Calloc(cs.min_indexspace,uint32_t);
      |                                                   ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195: construct_dc.o] Error 1
ERROR: compilation failed for package ‘TransView’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/TransView’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/TransView’