| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:37 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 2102/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.9.1 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
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. - 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: TargetSearch |
| Version: 2.9.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TargetSearch_2.9.1.tar.gz |
| StartedAt: 2024-11-25 07:11:19 -0500 (Mon, 25 Nov 2024) |
| EndedAt: 2024-11-25 07:16:17 -0500 (Mon, 25 Nov 2024) |
| EllapsedTime: 298.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TargetSearch_2.9.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TargetSearch.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.9.1’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 13.2.0-23ubuntu4) 13.2.0’
* 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 code 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 loading without being on the library search path ... 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 7.981 0.708 8.715
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Rinit.c -o Rinit.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c baseline.c -o baseline.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c detection.c -o detection.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c file.c -o file.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c find.c -o find.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c get_line.c -o get_line.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hpf.c -o hpf.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c matrix.c -o matrix.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c ncdf.c -o ncdf.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c peak.c -o peak.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c spectrum.c -o spectrum.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c strutils.c -o strutils.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find.o get_line.o hpf.o matrix.o ncdf.o peak.o spectrum.o strutils.o utils.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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", color=FALSE, verbose=1)
+ }
Loading required package: TargetSearchData
test_FindAllPeaks.R........... 19 tests OK 0.8s
FAMEs were saved in /tmp/Rtmpgc3w9i/file2be1356187e656.pdf
FAMEs were saved in /tmp/Rtmpgc3w9i/file2be1356187e656.pdf
FAMEs were saved in /tmp/Rtmpgc3w9i/file2be1356187e656.pdf
FAMEs were saved in /tmp/Rtmpgc3w9i/file2be1356187e656.pdf
test_fameoutliers.R........... 5 tests OK 55ms
test_file.R................... 4 tests OK 55ms
test_import_fame.R............ 14 tests OK 46ms
test_import_library.R......... 15 tests OK 81ms
test_ncdf4_plot_peak.R........ 7 tests OK 0.3s
test_quantMatrix.R............ 8 tests OK 28ms
test_ri_data_extract.R........ 6 tests OK 3.1s
test_ri_plot_peak.R........... 22 tests OK 96ms
test_tsLib.R.................. 24 tests OK 80ms
test_tsProfile.R.............. 12 tests OK 14ms
test_tsRim.R.................. 9 tests OK 4ms
test_tsSample.R............... 19 tests OK 28ms
test_write_ri_file.R.......... 6 tests OK 7ms
All ok, 170 results (4.7s)
>
> proc.time()
user system elapsed
4.904 0.094 4.990
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.059 | 0.003 | 0.062 | |
| FindAllPeaks | 0.585 | 0.019 | 0.626 | |
| FindPeaks | 0.107 | 0.000 | 0.107 | |
| ImportFameSettings | 0.006 | 0.002 | 0.008 | |
| ImportLibrary | 0.014 | 0.002 | 0.017 | |
| ImportSamples | 0.009 | 0.001 | 0.010 | |
| NetCDFPeakFinding | 0.128 | 0.038 | 0.167 | |
| Profile | 0.479 | 0.006 | 0.486 | |
| ProfileCleanUp | 0.386 | 0.028 | 0.414 | |
| RIcorrect | 7.981 | 0.708 | 8.715 | |
| TSExample | 1.530 | 0.098 | 1.629 | |
| Write.Results | 0.043 | 0.002 | 0.045 | |
| baseline | 0.197 | 0.010 | 0.207 | |
| baselineCorrection | 0.205 | 0.007 | 0.212 | |
| baselineCorrectionQuant | 0.273 | 0.006 | 0.280 | |
| checkRimLim | 0.631 | 0.090 | 0.721 | |
| file | 0.052 | 0.005 | 0.057 | |
| fixRI | 0.608 | 0.048 | 0.656 | |
| makeIndex | 0.002 | 0.000 | 0.004 | |
| medianRILib | 0.207 | 0.002 | 0.210 | |
| ncdf4Convert-method | 0.070 | 0.018 | 0.088 | |
| ncdf4_convert | 0.019 | 0.006 | 0.025 | |
| ncdf4_convert_from_path | 1.504 | 0.080 | 1.583 | |
| ncdf4_data_extract | 0.285 | 0.018 | 0.303 | |
| ncdf4_plot_peak | 0.821 | 0.046 | 0.867 | |
| ncdf4_update_ri | 0.206 | 0.009 | 0.215 | |
| peakCDFextraction | 0.316 | 0.061 | 0.379 | |
| peakFind | 0.110 | 0.005 | 0.115 | |
| plotFAME | 0.006 | 0.001 | 0.007 | |
| plotPeak | 0.124 | 0.007 | 0.131 | |
| plotPeakRI | 0.399 | 0.009 | 0.408 | |
| plotPeakSimple | 0.220 | 0.023 | 0.243 | |
| plotRIdev | 0.226 | 0.005 | 0.231 | |
| plotRefSpectra | 0.075 | 0.001 | 0.076 | |
| plotSpectra | 0.114 | 0.004 | 0.118 | |
| quantMatrix | 0.373 | 0.009 | 0.382 | |
| ri2rt | 0.003 | 0.000 | 0.003 | |
| riMatrix | 0.530 | 0.067 | 0.597 | |
| ri_data_extract | 0.023 | 0.002 | 0.025 | |
| ri_plot_peak | 0.580 | 0.011 | 0.591 | |
| rt2ri | 0.003 | 0.000 | 0.003 | |
| sampleRI | 0.216 | 0.007 | 0.223 | |
| tsLib-class | 0.021 | 0.002 | 0.023 | |
| tsMSdata-class | 0.008 | 0.018 | 0.026 | |
| tsProfile-class | 0.005 | 0.004 | 0.009 | |
| tsRim-class | 0.002 | 0.001 | 0.003 | |
| tsSample-class | 0.017 | 0.002 | 0.019 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 0.790 | 0.059 | 0.849 | |
| writeLibText | 0.015 | 0.001 | 0.016 | |
| writeMSP | 0.012 | 0.002 | 0.014 | |