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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 727/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.60.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/flagme
git_branch: RELEASE_3_19
git_last_commit: e927a2c
git_last_commit_date: 2024-04-30 10:19:15 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for flagme on palomino3

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: 1.60.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings flagme_1.60.0.tar.gz
StartedAt: 2024-06-13 03:45:45 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:10:58 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 1512.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings flagme_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.60.0'
* 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 whether package 'flagme' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/flagme/libs/x64/flagme.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plotAlignedFrags                           37.77   2.77  118.70
corPrt                                     22.42   1.73   96.27
dynRT                                      22.74   1.41   96.26
addXCMSPeaks                               22.76   1.31   94.77
peaksAlignment-class                       21.55   1.42   93.05
plotAlignment-peaksAlignment-method        21.45   1.26   95.60
ndpRT                                      20.50   1.69  100.84
progressiveAlignment-class                 20.79   1.39   90.51
retFatMatrix                               20.18   1.36   91.05
plotFrags                                  19.00   1.45   87.02
imputePeaks                                11.62   0.69   13.50
plotChrom-peaksDataset-method               8.78   0.53    9.28
gatherInfo                                  8.06   0.36    8.39
multipleAlignment-class                     7.96   0.45    8.38
calcTimeDiffs                               7.72   0.64    8.71
rmaFitUnit                                  7.38   0.58    7.97
dp                                          7.17   0.44    7.59
clusterAlignment                            6.66   0.33    6.97
plotClustAlignment-clusterAlignment-method  6.43   0.29    6.67
normDotProduct                              6.08   0.30    6.34
addAMDISPeaks                               5.93   0.25    7.30
peaksDataset                                5.70   0.28    5.97
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck/00check.log'
for details.


Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL flagme
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'flagme' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dp.c -o dp.o
dp.c: In function 'dp':
dp.c:264:35: warning: 'tb' may be used uninitialized [-Wmaybe-uninitialized]
  264 |           phi[(i+1)+(j+1)*(nr+1)] = tb;
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
dp.c:217:30: note: 'tb' was declared here
  217 |   int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
      |                              ^~
dp.c:263:33: warning: 'cur_min' may be used uninitialized [-Wmaybe-uninitialized]
  263 |           D[(i+1)+(j+1)*(nr+1)] = cur_min;
      |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:218:21: note: 'cur_min' was declared here
  218 |   double gap=*gap_, cur_min, a, b, c;
      |                     ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pearson.c -o pearson.o
gcc -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-flagme/00new/flagme/libs/x64
** 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
** 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
addAMDISPeaks5.930.257.30
addChromaTOFPeaks3.560.303.84
addXCMSPeaks22.76 1.3194.77
betweenAlignment000
calcTimeDiffs7.720.648.71
clusterAlignment6.660.336.97
corPrt22.42 1.7396.27
dp7.170.447.59
dynRT22.74 1.4196.26
gatherInfo8.060.368.39
imputePeaks11.62 0.6913.50
multipleAlignment-class7.960.458.38
ndpRT 20.50 1.69100.84
normDotProduct6.080.306.34
parseChromaTOF2.510.063.58
parseELU2.050.002.05
peaksAlignment-class21.55 1.4293.05
peaksDataset5.700.285.97
plotAlignedFrags 37.77 2.77118.70
plotAlignment-peaksAlignment-method21.45 1.2695.60
plotChrom-peaksDataset-method8.780.539.28
plotClustAlignment-clusterAlignment-method6.430.296.67
plotFrags19.00 1.4587.02
plotImage4.350.224.58
progressiveAlignment-class20.79 1.3990.51
retFatMatrix20.18 1.3691.05
rmaFitUnit7.380.587.97