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) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 2169/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TransView 1.51.0 (landing page) Julius Muller
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
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: 1.51.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TransView |
| StartedAt: 2024-12-24 03:01:41 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 03:01:44 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 3.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TransView
###
##############################################################################
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* checking for file ‘TransView/DESCRIPTION’ ... OK
* preparing ‘TransView’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘TransView’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_TransView.c -o R_init_TransView.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bam_plbuf.c -o bam_plbuf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bin_density.c -o bin_density.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c construct_dc.c -o construct_dc.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include/htslib/hts.h:36,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include/htslib/sam.h:33,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include/samtools-1.7-compat.h:5,
from parse_sam.h:4,
from construct_dc.c:23:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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: error: 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: error: 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/R/R/etc/Makeconf:195: construct_dc.o] Error 1
ERROR: compilation failed for package ‘TransView’
* removing ‘/home/biocbuild/tmp/RtmpDcHqpE/Rinst3d930e15fabcc0/TransView’
-----------------------------------
ERROR: package installation failed