| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:42 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
To the developers/maintainers of the TargetSearch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TargetSearch.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2038/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.3.0 (landing page) Alvaro Cuadros-Inostroza
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: TargetSearch |
| Version: 2.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TargetSearch_2.3.0.tar.gz |
| StartedAt: 2023-05-10 06:47:53 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 06:49:15 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 82.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TargetSearch_2.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TargetSearch.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TargetSearch’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RIcorrect 8.81 0.513 9.528
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘RICorrection.Rnw’... OK
‘TargetSearch.Rnw’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Rinit.c -o Rinit.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c baseline.c -o baseline.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c detection.c -o detection.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c file.c -o file.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c find_peaks.c -o find_peaks.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c get_line.c -o get_line.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hpf.c -o hpf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c matrix.c -o matrix.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ncdf.c -o ncdf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c peak.c -o peak.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o gcc -shared -L/usr/local/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find_peaks.o get_line.o hpf.o matrix.o ncdf.o peak.o utils.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-TargetSearch/00new/TargetSearch/libs ** R ** data ** 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 (TargetSearch)
TargetSearch.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if ( requireNamespace("tinytest", quietly=TRUE) && requireNamespace("TargetSearchData", quietly=TRUE)) {
+ tinytest::test_package("TargetSearch")
+ }
Loading required package: TargetSearchData
test_file.R................... 0 tests
test_file.R................... 0 tests
test_file.R................... 0 tests
test_file.R................... 0 tests
test_file.R................... 1 tests [0;32mOK[0m
test_file.R................... 1 tests [0;32mOK[0m
test_file.R................... 1 tests [0;32mOK[0m
test_file.R................... 2 tests [0;32mOK[0m
test_file.R................... 2 tests [0;32mOK[0m
test_file.R................... 3 tests [0;32mOK[0m
test_file.R................... 3 tests [0;32mOK[0m
test_file.R................... 3 tests [0;32mOK[0m
test_file.R................... 4 tests [0;32mOK[0m [0;34m0.1s[0m
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 0 tests
test_ncdf4_plot_peak.R........ 5 tests [0;32mOK[0m
test_ncdf4_plot_peak.R........ 6 tests [0;32mOK[0m
test_ncdf4_plot_peak.R........ 7 tests [0;32mOK[0m
test_ncdf4_plot_peak.R........ 7 tests [0;32mOK[0m [0;34m0.5s[0m
test_quantMatrix.R............ 0 tests
test_quantMatrix.R............ 0 tests
test_quantMatrix.R............ 0 tests
test_quantMatrix.R............ 0 tests
test_quantMatrix.R............ 0 tests
test_quantMatrix.R............ 0 tests
test_quantMatrix.R............ 1 tests [0;32mOK[0m
test_quantMatrix.R............ 2 tests [0;32mOK[0m
test_quantMatrix.R............ 2 tests [0;32mOK[0m
test_quantMatrix.R............ 2 tests [0;32mOK[0m
test_quantMatrix.R............ 3 tests [0;32mOK[0m
test_quantMatrix.R............ 4 tests [0;32mOK[0m
test_quantMatrix.R............ 4 tests [0;32mOK[0m
test_quantMatrix.R............ 4 tests [0;32mOK[0m
test_quantMatrix.R............ 5 tests [0;32mOK[0m
test_quantMatrix.R............ 5 tests [0;32mOK[0m
test_quantMatrix.R............ 5 tests [0;32mOK[0m
test_quantMatrix.R............ 6 tests [0;32mOK[0m [0;36m60ms[0m
test_ri_data_extract.R........ 0 tests
test_ri_data_extract.R........ 0 tests
test_ri_data_extract.R........ 0 tests
test_ri_data_extract.R........ 0 tests
test_ri_data_extract.R........ 1 tests [0;32mOK[0m
test_ri_data_extract.R........ 1 tests [0;32mOK[0m
test_ri_data_extract.R........ 1 tests [0;32mOK[0m
test_ri_data_extract.R........ 2 tests [0;32mOK[0m
test_ri_data_extract.R........ 2 tests [0;32mOK[0m
test_ri_data_extract.R........ 2 tests [0;32mOK[0m
test_ri_data_extract.R........ 3 tests [0;32mOK[0m
test_ri_data_extract.R........ 3 tests [0;32mOK[0m
test_ri_data_extract.R........ 4 tests [0;32mOK[0m
test_ri_data_extract.R........ 4 tests [0;32mOK[0m
test_ri_data_extract.R........ 4 tests [0;32mOK[0m
test_ri_data_extract.R........ 4 tests [0;32mOK[0m
test_ri_data_extract.R........ 4 tests [0;32mOK[0m
test_ri_data_extract.R........ 4 tests [0;32mOK[0m
test_ri_data_extract.R........ 5 tests [0;32mOK[0m
test_ri_data_extract.R........ 5 tests [0;32mOK[0m
test_ri_data_extract.R........ 6 tests [0;32mOK[0m [0;34m0.3s[0m
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 0 tests
test_ri_plot_peak.R........... 10 tests [0;32mOK[0m
test_ri_plot_peak.R........... 11 tests [0;32mOK[0m
test_ri_plot_peak.R........... 12 tests [0;32mOK[0m
test_ri_plot_peak.R........... 12 tests [0;32mOK[0m [0;36m96ms[0m
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 0 tests
test_tsLib.R.................. 1 tests [0;32mOK[0m
test_tsLib.R.................. 2 tests [0;32mOK[0m
test_tsLib.R.................. 2 tests [0;32mOK[0m
test_tsLib.R.................. 2 tests [0;32mOK[0m
test_tsLib.R.................. 3 tests [0;32mOK[0m
test_tsLib.R.................. 4 tests [0;32mOK[0m
test_tsLib.R.................. 4 tests [0;32mOK[0m
test_tsLib.R.................. 5 tests [0;32mOK[0m
test_tsLib.R.................. 6 tests [0;32mOK[0m
test_tsLib.R.................. 7 tests [0;32mOK[0m
test_tsLib.R.................. 8 tests [0;32mOK[0m
test_tsLib.R.................. 9 tests [0;32mOK[0m
test_tsLib.R.................. 10 tests [0;32mOK[0m
test_tsLib.R.................. 11 tests [0;32mOK[0m
test_tsLib.R.................. 12 tests [0;32mOK[0m [0;36m67ms[0m
test_tsRim.R.................. 0 tests
test_tsRim.R.................. 1 tests [0;32mOK[0m
test_tsRim.R.................. 2 tests [0;32mOK[0m
test_tsRim.R.................. 2 tests [0;32mOK[0m
test_tsRim.R.................. 3 tests [0;32mOK[0m
test_tsRim.R.................. 4 tests [0;32mOK[0m
test_tsRim.R.................. 4 tests [0;32mOK[0m
test_tsRim.R.................. 5 tests [0;32mOK[0m
test_tsRim.R.................. 6 tests [0;32mOK[0m [0;36m6ms[0m
test_tsSample.R............... 0 tests
test_tsSample.R............... 0 tests
test_tsSample.R............... 0 tests
test_tsSample.R............... 1 tests [0;32mOK[0m
test_tsSample.R............... 2 tests [0;32mOK[0m
test_tsSample.R............... 3 tests [0;32mOK[0m
test_tsSample.R............... 3 tests [0;32mOK[0m
test_tsSample.R............... 3 tests [0;32mOK[0m
test_tsSample.R............... 3 tests [0;32mOK[0m
test_tsSample.R............... 4 tests [0;32mOK[0m
test_tsSample.R............... 5 tests [0;32mOK[0m
test_tsSample.R............... 6 tests [0;32mOK[0m
test_tsSample.R............... 6 tests [0;32mOK[0m
test_tsSample.R............... 7 tests [0;32mOK[0m
test_tsSample.R............... 8 tests [0;32mOK[0m
test_tsSample.R............... 9 tests [0;32mOK[0m [0;36m42ms[0m
All ok, 62 results (1.1s)
>
> proc.time()
user system elapsed
1.429 0.087 1.501
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.043 | 0.000 | 0.043 | |
| FindAllPeaks | 0.472 | 0.033 | 0.532 | |
| FindPeaks | 0.130 | 0.000 | 0.131 | |
| ImportFameSettings | 0.008 | 0.004 | 0.012 | |
| ImportLibrary | 0.027 | 0.000 | 0.027 | |
| ImportSamples | 0.013 | 0.000 | 0.014 | |
| NetCDFPeakFinding | 0.115 | 0.023 | 0.154 | |
| Profile | 0.694 | 0.012 | 0.707 | |
| ProfileCleanUp | 0.507 | 0.020 | 0.530 | |
| RIcorrect | 8.810 | 0.513 | 9.528 | |
| TSExample | 1.825 | 0.044 | 1.869 | |
| Write.Results | 0.058 | 0.000 | 0.059 | |
| baseline | 0.210 | 0.020 | 0.231 | |
| baselineCorrection | 0.252 | 0.000 | 0.252 | |
| baselineCorrectionQuant | 0.292 | 0.008 | 0.301 | |
| checkRimLim | 0.603 | 0.008 | 0.611 | |
| file | 0.049 | 0.012 | 0.061 | |
| fixRI | 0.705 | 0.028 | 0.732 | |
| medianRILib | 0.271 | 0.000 | 0.271 | |
| ncdf4Convert-method | 0.088 | 0.004 | 0.092 | |
| ncdf4_convert | 0.028 | 0.000 | 0.027 | |
| ncdf4_convert_from_path | 1.597 | 0.132 | 1.729 | |
| ncdf4_data_extract | 0.308 | 0.032 | 0.340 | |
| ncdf4_plot_peak | 0.865 | 0.040 | 0.906 | |
| ncdf4_update_ri | 0.219 | 0.000 | 0.219 | |
| peakCDFextraction | 0.324 | 0.020 | 0.344 | |
| peakFind | 0.138 | 0.004 | 0.142 | |
| plotFAME | 0.006 | 0.012 | 0.018 | |
| plotPeak | 0.113 | 0.092 | 0.206 | |
| plotPeakRI | 0.382 | 0.032 | 0.414 | |
| plotPeakSimple | 0.227 | 0.012 | 0.238 | |
| plotRIdev | 0.327 | 0.028 | 0.354 | |
| plotSpectra | 0.157 | 0.004 | 0.160 | |
| quantMatrix | 0.501 | 0.020 | 0.521 | |
| ri2rt | 0.006 | 0.000 | 0.006 | |
| riMatrix | 0.560 | 0.056 | 0.617 | |
| ri_data_extract | 0.031 | 0.000 | 0.031 | |
| ri_plot_peak | 0.740 | 0.020 | 0.761 | |
| rt2ri | 0.001 | 0.003 | 0.004 | |
| sampleRI | 0.281 | 0.008 | 0.288 | |
| tsLib-class | 0.031 | 0.000 | 0.030 | |
| tsMSdata-class | 0.006 | 0.012 | 0.018 | |
| tsProfile-class | 0.010 | 0.000 | 0.011 | |
| tsRim-class | 0.003 | 0.000 | 0.003 | |
| tsSample-class | 0.021 | 0.004 | 0.026 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 1.139 | 0.061 | 1.202 | |
| writeLibText | 0.018 | 0.004 | 0.022 | |
| writeMSP | 0.02 | 0.00 | 0.02 | |