| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:55 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 2023/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.0.0 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TargetSearch |
| Version: 2.0.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TargetSearch.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings TargetSearch_2.0.0.tar.gz |
| StartedAt: 2023-04-11 06:40:54 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 06:42:20 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 85.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TargetSearch.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings TargetSearch_2.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/TargetSearch.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.0.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/TargetSearch/libs/x64/TargetSearch.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 7.81 1.28 12.83
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/TargetSearch.Rcheck/00check.log'
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'TargetSearch' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c baseline.c -o baseline.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection.c -o detection.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c file.c -o file.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c find_peaks.c -o find_peaks.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getLine.c -o getLine.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hpf.c -o hpf.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix.c -o matrix.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ncdf.c -o ncdf.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c peak.c -o peak.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -shared -s -static-libgcc -o TargetSearch.dll tmp.def Rinit.o baseline.o detection.o file.o find_peaks.o getLine.o hpf.o matrix.o ncdf.o peak.o utils.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-TargetSearch/00new/TargetSearch/libs/x64 ** 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 ** 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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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;34m0.4s[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;34m0.1s[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;34m0.6s[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
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;36m44ms[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;36m5ms[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;36m33ms[0m
All ok, 62 results (1.5s)
>
> proc.time()
user system elapsed
1.65 0.15 1.92
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.06 | 0.02 | 0.08 | |
| FindAllPeaks | 1.02 | 0.11 | 1.33 | |
| FindPeaks | 0.31 | 0.02 | 0.32 | |
| ImportFameSettings | 0.00 | 0.00 | 0.02 | |
| ImportLibrary | 0.04 | 0.00 | 0.05 | |
| ImportSamples | 0.00 | 0.00 | 0.01 | |
| NetCDFPeakFinding | 0.16 | 0.00 | 0.25 | |
| Profile | 0.95 | 0.04 | 1.00 | |
| ProfileCleanUp | 0.77 | 0.05 | 0.81 | |
| RIcorrect | 7.81 | 1.28 | 12.83 | |
| TSExample | 1.53 | 0.19 | 1.72 | |
| Write.Results | 0.11 | 0.00 | 0.11 | |
| baseline | 0.19 | 0.01 | 0.20 | |
| baselineCorrection | 0.23 | 0.00 | 0.23 | |
| baselineCorrectionQuant | 0.30 | 0.02 | 0.32 | |
| checkRimLim | 0.72 | 0.09 | 0.81 | |
| file | 0.09 | 0.00 | 0.11 | |
| fixRI | 0.78 | 0.10 | 0.88 | |
| medianRILib | 0.64 | 0.03 | 0.67 | |
| ncdf4Convert-method | 0.06 | 0.03 | 0.09 | |
| ncdf4_convert | 0.03 | 0.00 | 0.04 | |
| ncdf4_convert_from_path | 1.67 | 0.17 | 1.93 | |
| ncdf4_data_extract | 0.36 | 0.02 | 0.39 | |
| ncdf4_plot_peak | 0.86 | 0.11 | 0.99 | |
| ncdf4_update_ri | 0.16 | 0.03 | 0.20 | |
| peakCDFextraction | 0.33 | 0.06 | 0.39 | |
| peakFind | 0.27 | 0.02 | 0.28 | |
| plotFAME | 0.01 | 0.00 | 0.01 | |
| plotPeak | 0.11 | 0.01 | 0.13 | |
| plotPeakRI | 0.67 | 0.08 | 0.75 | |
| plotPeakSimple | 0.18 | 0.05 | 0.22 | |
| plotRIdev | 0.35 | 0.06 | 0.41 | |
| plotSpectra | 0.27 | 0.00 | 0.26 | |
| quantMatrix | 0.73 | 0.06 | 0.80 | |
| ri2rt | 0.02 | 0.00 | 0.01 | |
| riMatrix | 0.51 | 0.08 | 0.60 | |
| ri_data_extract | 0.08 | 0.00 | 0.08 | |
| ri_plot_peak | 1.42 | 0.06 | 1.49 | |
| rt2ri | 0 | 0 | 0 | |
| sampleRI | 0.50 | 0.03 | 0.53 | |
| tsLib-class | 0.03 | 0.00 | 0.03 | |
| tsMSdata-class | 0.00 | 0.02 | 0.01 | |
| tsProfile-class | 0.01 | 0.00 | 0.02 | |
| tsRim-class | 0.02 | 0.00 | 0.01 | |
| tsSample-class | 0.03 | 0.00 | 0.04 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 0.92 | 0.11 | 1.06 | |
| writeLibText | 0.02 | 0.01 | 0.03 | |
| writeMSP | 0.03 | 0.00 | 0.03 | |