| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:58 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1983/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 1.52.0 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TargetSearch |
| Version: 1.52.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TargetSearch_1.52.0.tar.gz |
| StartedAt: 2022-10-18 22:07:21 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 22:08:10 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 48.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TargetSearch_1.52.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TargetSearch.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘1.52.0’
* 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
* 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 7.904 0.781 8.714
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.15-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rinit.c -o Rinit.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c baseline.c -o baseline.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c detection.c -o detection.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c file.c -o file.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c find_peaks.c -o find_peaks.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c getLine.c -o getLine.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hpf.c -o hpf.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matrix.c -o matrix.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ncdf.c -o ncdf.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c peak.c -o peak.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find_peaks.o getLine.o hpf.o matrix.o ncdf.o peak.o utils.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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;34m0.3s[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;34m0.2s[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;36m65ms[0m
All ok, 29 results (0.7s)
>
> proc.time()
user system elapsed
0.891 0.069 0.944
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.027 | 0.008 | 0.035 | |
| FindAllPeaks | 0.353 | 0.044 | 0.415 | |
| FindPeaks | 0.100 | 0.004 | 0.103 | |
| ImportFameSettings | 0.007 | 0.000 | 0.008 | |
| ImportLibrary | 0.014 | 0.000 | 0.014 | |
| ImportSamples | 0.005 | 0.000 | 0.005 | |
| NetCDFPeakFinding | 0.127 | 0.027 | 0.156 | |
| Profile | 0.456 | 0.020 | 0.476 | |
| ProfileCleanUp | 0.404 | 0.016 | 0.420 | |
| RIcorrect | 7.904 | 0.781 | 8.714 | |
| TSExample | 1.454 | 0.068 | 1.522 | |
| checkRimLim | 0.547 | 0.068 | 0.615 | |
| file | 0.058 | 0.005 | 0.062 | |
| fixRI | 0.582 | 0.032 | 0.614 | |
| medianRILib | 0.178 | 0.016 | 0.195 | |
| ncdf4Convert-method | 0.056 | 0.008 | 0.064 | |
| ncdf4_convert | 0.012 | 0.006 | 0.019 | |
| ncdf4_convert_from_path | 0.001 | 0.000 | 0.001 | |
| ncdf4_data_extract | 0.001 | 0.001 | 0.001 | |
| ncdf4_plot_peak | 0.744 | 0.024 | 0.768 | |
| peakFind | 0.098 | 0.011 | 0.109 | |
| plotFAME | 0.013 | 0.000 | 0.013 | |
| plotPeak | 0.112 | 0.016 | 0.128 | |
| plotPeakRI | 0.262 | 0.016 | 0.278 | |
| plotPeakSimple | 0.213 | 0.008 | 0.221 | |
| plotRIdev | 0.233 | 0.000 | 0.234 | |
| plotSpectra | 0.117 | 0.000 | 0.118 | |
| quantMatrix | 0.347 | 0.012 | 0.359 | |
| ri2rt | 0.003 | 0.000 | 0.003 | |
| riMatrix | 0.557 | 0.040 | 0.598 | |
| ri_data_extract | 0.024 | 0.000 | 0.024 | |
| ri_plot_peak | 0.520 | 0.028 | 0.549 | |
| rt2ri | 0.003 | 0.000 | 0.003 | |
| sampleRI | 0.199 | 0.008 | 0.207 | |
| tsLib-class | 0.011 | 0.004 | 0.015 | |
| tsMSdata-class | 0.001 | 0.000 | 0.001 | |
| tsProfile-class | 0.001 | 0.000 | 0.001 | |
| tsRim-class | 0.002 | 0.000 | 0.002 | |
| tsSample-class | 0.019 | 0.001 | 0.020 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 0.935 | 0.013 | 0.948 | |
| writeLibText | 0.010 | 0.004 | 0.013 | |