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This page was generated on 2024-05-04 11:40:31 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for flagme on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: flagme
Version: 1.60.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings flagme_1.60.0.tar.gz
StartedAt: 2024-05-04 07:33:02 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 07:50:40 -0000 (Sat, 04 May 2024)
EllapsedTime: 1057.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings flagme_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flagme’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
plotAlignedFrags                           118.707 17.256  72.556
addXCMSPeaks                                65.703 10.809  55.517
peaksAlignment-class                        61.961 12.076  51.710
corPrt                                      61.093 11.388  52.320
plotAlignment-peaksAlignment-method         59.753 10.417  49.493
retFatMatrix                                62.136  7.762  49.714
progressiveAlignment-class                  59.080  9.540  48.619
dynRT                                       59.501  8.695  47.807
plotFrags                                   58.874  9.071  48.041
ndpRT                                       60.212  7.388  47.177
imputePeaks                                 14.994  0.259  15.314
plotChrom-peaksDataset-method               12.152  0.172  12.349
rmaFitUnit                                  11.201  0.212  11.435
multipleAlignment-class                     10.079  0.156  10.254
gatherInfo                                   9.994  0.192  10.206
calcTimeDiffs                                9.948  0.183  10.151
dp                                           9.034  0.423   9.477
plotClustAlignment-clusterAlignment-method   8.857  0.116   8.992
normDotProduct                               8.013  0.124   8.153
peaksDataset                                 7.568  0.427   8.012
clusterAlignment                             7.773  0.096   7.885
addAMDISPeaks                                7.494  0.239   7.783
plotImage                                    5.979  0.444   6.436
addChromaTOFPeaks                            5.076  0.136   5.221
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/flagme.Rcheck/00check.log’
for details.


Installation output

flagme.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL flagme
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:263:26: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  263 |    D[(i+1)+(j+1)*(nr+1)] = cur_min;
      |    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:264:28: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  264 |    phi[(i+1)+(j+1)*(nr+1)] = tb;
      |    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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
addAMDISPeaks7.4940.2397.783
addChromaTOFPeaks5.0760.1365.221
addXCMSPeaks65.70310.80955.517
betweenAlignment0.0010.0000.000
calcTimeDiffs 9.948 0.18310.151
clusterAlignment7.7730.0967.885
corPrt61.09311.38852.320
dp9.0340.4239.477
dynRT59.501 8.69547.807
gatherInfo 9.994 0.19210.206
imputePeaks14.994 0.25915.314
multipleAlignment-class10.079 0.15610.254
ndpRT60.212 7.38847.177
normDotProduct8.0130.1248.153
parseChromaTOF2.9300.0362.972
parseELU2.6990.0122.716
peaksAlignment-class61.96112.07651.710
peaksDataset7.5680.4278.012
plotAlignedFrags118.707 17.256 72.556
plotAlignment-peaksAlignment-method59.75310.41749.493
plotChrom-peaksDataset-method12.152 0.17212.349
plotClustAlignment-clusterAlignment-method8.8570.1168.992
plotFrags58.874 9.07148.041
plotImage5.9790.4446.436
progressiveAlignment-class59.080 9.54048.619
retFatMatrix62.136 7.76249.714
rmaFitUnit11.201 0.21211.435