Ben Bolstad
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/affyPLM |
| git_branch: devel |
| git_last_commit: 9c743e0 |
| git_last_commit_date: 2023-10-24 09:32:34 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:09 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 30/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyPLM 1.79.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the affyPLM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyPLM.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. |
| Package: affyPLM |
| Version: 1.79.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL affyPLM |
| StartedAt: 2024-03-27 15:17:04 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:17:30 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 25.7 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL affyPLM
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘affyPLM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function ‘do_PLM_rlm’:
do_PLMrlm.c:620:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
620 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function ‘do_PLMrma’:
do_PLMrma.c:209:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
209 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function ‘do_PLMthreestep’:
do_PLMthreestep.c:118:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
118 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function ‘IdealMM_correct_single’:
idealmismatch.c:71:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
71 | int first_ind;
| ^~~~~~~~~
idealmismatch.c: In function ‘SpecificBiweightCorrect_single’:
idealmismatch.c:183:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
183 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o
preprocess.c: In function ‘pp_background’:
preprocess.c:158:7: warning: variable ‘which_lesn’ set but not used [-Wunused-but-set-variable]
158 | int which_lesn;
| ^~~~~~~~~~
preprocess.c: In function ‘pp_bothstages’:
preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
677 | int rows,cols;
| ^~~~
preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
677 | int rows,cols;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function ‘qnorm_probeset_c’:
qnorm_probeset.c:110:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
110 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function ‘R_rlm_PLMset_c’:
rlm_PLM.c:1481:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
1481 | int rows,cols;
| ^~~~
rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
1481 | int rows,cols;
| ^~~~
rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’:
rlm_PLM.c:868:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
868 | snprintf(tmp_str2,9,"%d",j+2);
| ^~
rlm_PLM.c:868:31: note: directive argument in the range [2, 2147483647]
868 | snprintf(tmp_str2,9,"%d",j+2);
| ^~~~
In file included from /usr/include/stdio.h:894,
from /home/biocbuild/bbs-3.19-bioc/R/include/R.h:44,
from preprocess.h:4,
from rlm_PLM.c:71:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function ‘median’:
rma_common.c:60:7: warning: unused variable ‘i’ [-Wunused-variable]
60 | int i;
| ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep.c -o threestep.o
threestep.c: In function ‘threestep_summary’:
threestep.c:82:15: warning: variable ‘MM’ set but not used [-Wunused-but-set-variable]
82 | double *PM,*MM;
| ^~
threestep.c: In function ‘R_threestep_c’:
threestep.c:193:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
193 | int rows,cols;
| ^~~~
threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
193 | int rows,cols;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function ‘do_3summary’:
threestep_summary.c:73:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
73 | int first_ind;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c transfns.c -o transfns.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-affyPLM/00new/affyPLM/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 (affyPLM)