| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1895/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 1.48.0 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TargetSearch |
| Version: 1.48.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TargetSearch_1.48.0.tar.gz |
| StartedAt: 2021-10-15 00:36:17 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:37:53 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 95.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TargetSearch_1.48.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TargetSearch.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.48.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 16.47 1.275 17.861
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c baseline.c -o baseline.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c detection.c -o detection.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c file.c -o file.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c find_peaks.c -o find_peaks.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c getLine.c -o getLine.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hpf.c -o hpf.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c matrix.c -o matrix.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ncdf.c -o ncdf.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c peak.c -o peak.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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 ‘RICorrection.Rnw’ ‘TargetSearch.Rnw’ ** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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;34m0.2s[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;34m0.6s[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;34m0.7s[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;34m0.1s[0m
All ok, 29 results (1.7s)
>
> proc.time()
user system elapsed
2.119 0.169 2.271
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.057 | 0.010 | 0.107 | |
| FindAllPeaks | 1.274 | 0.054 | 1.340 | |
| FindPeaks | 0.366 | 0.009 | 0.374 | |
| ImportFameSettings | 0.008 | 0.001 | 0.009 | |
| ImportLibrary | 0.037 | 0.001 | 0.039 | |
| ImportSamples | 0.008 | 0.002 | 0.010 | |
| NetCDFPeakFinding | 0.346 | 0.035 | 0.382 | |
| Profile | 1.767 | 0.039 | 1.809 | |
| ProfileCleanUp | 1.577 | 0.034 | 1.612 | |
| RIcorrect | 16.470 | 1.275 | 17.861 | |
| TSExample | 2.097 | 0.198 | 2.337 | |
| checkRimLim | 0.710 | 0.030 | 0.741 | |
| file | 0.147 | 0.013 | 0.160 | |
| fixRI | 1.531 | 0.074 | 1.606 | |
| medianRILib | 0.908 | 0.024 | 0.933 | |
| ncdf4Convert-method | 0.112 | 0.004 | 0.116 | |
| ncdf4_convert | 0.039 | 0.002 | 0.041 | |
| ncdf4_convert_from_path | 0.000 | 0.001 | 0.000 | |
| ncdf4_data_extract | 0.000 | 0.000 | 0.001 | |
| ncdf4_plot_peak | 1.646 | 0.107 | 1.798 | |
| peakFind | 0.493 | 0.015 | 0.509 | |
| plotFAME | 0.014 | 0.003 | 0.017 | |
| plotPeak | 0.351 | 0.013 | 0.365 | |
| plotPeakRI | 1.365 | 0.044 | 1.412 | |
| plotPeakSimple | 0.625 | 0.030 | 0.660 | |
| plotRIdev | 0.720 | 0.023 | 0.745 | |
| plotSpectra | 0.503 | 0.015 | 0.519 | |
| quantMatrix | 1.526 | 0.041 | 1.567 | |
| ri2rt | 0.005 | 0.001 | 0.006 | |
| riMatrix | 1.344 | 0.078 | 1.422 | |
| ri_data_extract | 0.098 | 0.003 | 0.101 | |
| ri_plot_peak | 2.790 | 0.081 | 2.876 | |
| rt2ri | 0.006 | 0.000 | 0.007 | |
| sampleRI | 0.952 | 0.021 | 0.974 | |
| tsLib-class | 0.029 | 0.007 | 0.035 | |
| tsMSdata-class | 0.001 | 0.001 | 0.002 | |
| tsProfile-class | 0.001 | 0.002 | 0.002 | |
| tsRim-class | 0.002 | 0.001 | 0.003 | |
| tsSample-class | 0.026 | 0.004 | 0.029 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 1.377 | 0.100 | 1.478 | |
| writeLibText | 0.020 | 0.002 | 0.021 | |