| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 2120/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.8.0 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: TargetSearch |
| Version: 2.8.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TargetSearch_2.8.0.tar.gz |
| StartedAt: 2025-01-09 00:58:31 -0000 (Thu, 09 Jan 2025) |
| EndedAt: 2025-01-09 00:59:35 -0000 (Thu, 09 Jan 2025) |
| EllapsedTime: 64.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TargetSearch_2.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TargetSearch.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.8.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 9.152 0.192 9.365
* 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 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-3.20-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Rinit.c -o Rinit.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c baseline.c -o baseline.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c detection.c -o detection.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c file.c -o file.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c find.c -o find.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c get_line.c -o get_line.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c hpf.c -o hpf.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c matrix.c -o matrix.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ncdf.c -o ncdf.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c peak.c -o peak.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c spectrum.c -o spectrum.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c strutils.c -o strutils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/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/R/R/lib -lR installing to /home/biocbuild/R/R-4.4.2/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 1.0s
FAMEs were saved in /home/biocbuild/tmp/RtmpuiUDTj/file3e20e855dd8e2b.pdf
FAMEs were saved in /home/biocbuild/tmp/RtmpuiUDTj/file3e20e855dd8e2b.pdf
FAMEs were saved in /home/biocbuild/tmp/RtmpuiUDTj/file3e20e855dd8e2b.pdf
FAMEs were saved in /home/biocbuild/tmp/RtmpuiUDTj/file3e20e855dd8e2b.pdf
test_fameoutliers.R........... 5 tests OK 77ms
test_file.R................... 4 tests OK 61ms
test_import_fame.R............ 14 tests OK 18ms
test_import_library.R......... 15 tests OK 0.2s
test_ncdf4_plot_peak.R........ 7 tests OK 0.5s
test_quantMatrix.R............ 8 tests OK 60ms
test_ri_data_extract.R........ 6 tests OK 4.4s
test_ri_plot_peak.R........... 22 tests OK 0.1s
test_tsLib.R.................. 24 tests OK 0.1s
test_tsProfile.R.............. 12 tests OK 18ms
test_tsRim.R.................. 9 tests OK 6ms
test_tsSample.R............... 19 tests OK 42ms
test_write_ri_file.R.......... 6 tests OK 26ms
All ok, 170 results (6.6s)
>
> proc.time()
user system elapsed
6.717 0.173 6.906
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.075 | 0.000 | 0.076 | |
| FindAllPeaks | 0.624 | 0.004 | 0.629 | |
| FindPeaks | 0.109 | 0.004 | 0.113 | |
| ImportFameSettings | 0.009 | 0.000 | 0.009 | |
| ImportLibrary | 0.022 | 0.000 | 0.023 | |
| ImportSamples | 0.011 | 0.003 | 0.014 | |
| NetCDFPeakFinding | 0.122 | 0.008 | 0.131 | |
| Profile | 0.585 | 0.016 | 0.602 | |
| ProfileCleanUp | 0.462 | 0.004 | 0.468 | |
| RIcorrect | 9.152 | 0.192 | 9.365 | |
| TSExample | 1.988 | 0.024 | 2.016 | |
| Write.Results | 0.059 | 0.000 | 0.059 | |
| baseline | 0.210 | 0.004 | 0.214 | |
| baselineCorrection | 0.229 | 0.000 | 0.228 | |
| baselineCorrectionQuant | 0.29 | 0.00 | 0.29 | |
| checkRimLim | 0.608 | 0.020 | 0.629 | |
| file | 0.053 | 0.004 | 0.058 | |
| fixRI | 0.634 | 0.028 | 0.664 | |
| medianRILib | 0.234 | 0.000 | 0.234 | |
| ncdf4Convert-method | 0.080 | 0.004 | 0.084 | |
| ncdf4_convert | 0.026 | 0.000 | 0.026 | |
| ncdf4_convert_from_path | 1.490 | 0.040 | 1.535 | |
| ncdf4_data_extract | 0.316 | 0.004 | 0.321 | |
| ncdf4_plot_peak | 0.910 | 0.008 | 0.919 | |
| ncdf4_update_ri | 0.202 | 0.003 | 0.207 | |
| peakCDFextraction | 0.318 | 0.004 | 0.322 | |
| peakFind | 0.125 | 0.000 | 0.125 | |
| plotFAME | 0.008 | 0.000 | 0.008 | |
| plotPeak | 0.125 | 0.000 | 0.124 | |
| plotPeakRI | 0.429 | 0.020 | 0.450 | |
| plotPeakSimple | 0.204 | 0.008 | 0.211 | |
| plotRIdev | 0.302 | 0.000 | 0.303 | |
| plotRefSpectra | 0.099 | 0.004 | 0.102 | |
| plotSpectra | 0.121 | 0.012 | 0.133 | |
| quantMatrix | 0.451 | 0.008 | 0.460 | |
| ri2rt | 0.004 | 0.000 | 0.004 | |
| riMatrix | 0.542 | 0.016 | 0.560 | |
| ri_data_extract | 0.024 | 0.004 | 0.027 | |
| ri_plot_peak | 0.648 | 0.004 | 0.654 | |
| rt2ri | 0.004 | 0.000 | 0.004 | |
| sampleRI | 0.255 | 0.000 | 0.255 | |
| tsLib-class | 0.018 | 0.004 | 0.022 | |
| tsMSdata-class | 0.01 | 0.00 | 0.01 | |
| tsProfile-class | 0.008 | 0.000 | 0.008 | |
| tsRim-class | 0.002 | 0.000 | 0.002 | |
| tsSample-class | 0.024 | 0.000 | 0.024 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 1.074 | 0.012 | 1.090 | |
| writeLibText | 0.021 | 0.000 | 0.021 | |
| writeMSP | 0.017 | 0.000 | 0.018 | |