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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 720/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.62.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/flagme
git_branch: RELEASE_3_20
git_last_commit: 8706d82
git_last_commit_date: 2024-10-29 09:30:34 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation


CHECK results for flagme on merida1

To the developers/maintainers of the flagme package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.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.

raw results


Summary

Package: flagme
Version: 1.62.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.62.0.tar.gz
StartedAt: 2024-12-20 03:28:10 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:53:40 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1529.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.62.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.62.0’
* package encoding: UTF-8
* 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 ‘flagme’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘xcms:::rectUnique’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addXCMSPeaks: no visible global function definition for ‘bpparam’
addXCMSPeaks: no visible global function definition for ‘sampnames’
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘setNames’
importSpec : <anonymous>: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  bpparam sampnames setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'addXCMSPeaks.Rd':
  ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’
  ‘[xcms]{peaksDataset}’

Missing link or links in Rd file 'plotAlignment-peaksAlignment-method.Rd':
  ‘plotAlignment’

Missing link or links in Rd file 'plotClustAlignment-clusterAlignment-method.Rd':
  ‘plotAlignment’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
plotAlignedFrags                           152.190 32.934 103.673
addXCMSPeaks                                80.869 16.447  72.081
corPrt                                      78.787 17.384  70.559
peaksAlignment-class                        78.252 16.979  70.365
progressiveAlignment-class                  77.359 17.077  68.069
dynRT                                       76.982 17.121  67.852
ndpRT                                       76.747 16.988  68.020
retFatMatrix                                76.907 16.808  67.602
plotAlignment-peaksAlignment-method         76.409 17.043  69.181
plotFrags                                   75.585 17.015  66.887
imputePeaks                                 18.696  0.297  19.464
plotChrom-peaksDataset-method               16.509  0.338  17.098
calcTimeDiffs                               13.133  0.347  13.761
gatherInfo                                  12.287  0.266  12.655
rmaFitUnit                                  12.046  0.328  12.450
multipleAlignment-class                     12.189  0.167  12.800
dp                                          11.345  0.221  11.625
clusterAlignment                            11.193  0.202  11.493
normDotProduct                              10.239  0.219  10.702
plotClustAlignment-clusterAlignment-method  10.156  0.204  10.772
addAMDISPeaks                                9.580  0.299  10.132
peaksDataset                                 9.439  0.210   9.979
addChromaTOFPeaks                            7.228  0.275   7.732
plotImage                                    6.131  0.165   6.476
parseChromaTOF                               5.606  0.054   5.749
parseELU                                     5.121  0.027   5.398
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck/00check.log’
for details.


Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flagme
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dp.c -o dp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pearson.c -o pearson.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-flagme/00new/flagme/libs
** R
** 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 (flagme)

Tests output


Example timings

flagme.Rcheck/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks 9.580 0.29910.132
addChromaTOFPeaks7.2280.2757.732
addXCMSPeaks80.86916.44772.081
betweenAlignment0.0000.0010.001
calcTimeDiffs13.133 0.34713.761
clusterAlignment11.193 0.20211.493
corPrt78.78717.38470.559
dp11.345 0.22111.625
dynRT76.98217.12167.852
gatherInfo12.287 0.26612.655
imputePeaks18.696 0.29719.464
multipleAlignment-class12.189 0.16712.800
ndpRT76.74716.98868.020
normDotProduct10.239 0.21910.702
parseChromaTOF5.6060.0545.749
parseELU5.1210.0275.398
peaksAlignment-class78.25216.97970.365
peaksDataset9.4390.2109.979
plotAlignedFrags152.190 32.934103.673
plotAlignment-peaksAlignment-method76.40917.04369.181
plotChrom-peaksDataset-method16.509 0.33817.098
plotClustAlignment-clusterAlignment-method10.156 0.20410.772
plotFrags75.58517.01566.887
plotImage6.1310.1656.476
progressiveAlignment-class77.35917.07768.069
retFatMatrix76.90716.80867.602
rmaFitUnit12.046 0.32812.450