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This page was generated on 2024-05-04 11:37:00 -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 1630/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ptairMS 1.12.0  (landing page)
camille Roquencourt
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ptairMS
git_branch: RELEASE_3_19
git_last_commit: b288c6e
git_last_commit_date: 2024-04-30 11:33:01 -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 ptairMS on nebbiolo1


To the developers/maintainers of the ptairMS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ptairMS.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: ptairMS
Version: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ptairMS_1.12.0.tar.gz
StartedAt: 2024-05-04 02:34:44 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:45:06 -0400 (Sat, 04 May 2024)
EllapsedTime: 621.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ptairMS.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ptairMS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.12.0’
* 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 ‘ptairMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
See ‘/home/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘htmlwidgets’ ‘plyr’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’
  ‘processFileTemporalNominalMass’ ‘tofToMz’
* 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 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
detectPeak           79.932  0.548  80.482
writeEset            15.075  0.120  15.195
alignSamples         14.556  0.332  14.899
impute               14.273  0.144  14.419
imputeMat            14.073  0.112  14.184
getPeakList          13.466  0.136  13.603
annotation           13.046  0.281  13.327
convert_to_mzML      11.937  0.449  12.385
plotTIC              11.175  0.100  11.274
plot                 11.112  0.056  11.169
plotRaw              10.281  0.104  10.385
plotFeatures         10.253  0.080  10.333
setSampleMetadata     9.949  0.080  10.030
defineKnots           9.689  0.128   9.818
resetSampleMetadata   9.250  0.084   9.335
rmPeakList            9.199  0.084   9.282
getSampleMetadata     9.054  0.104   9.158
updatePtrSet          9.050  0.080   9.130
exportSampleMetada    8.983  0.120   9.103
importSampleMetadata  9.006  0.080   9.087
plotCalib             8.727  0.075   8.803
getDirectory          8.535  0.072   8.607
createPtrSet          8.208  0.111   8.333
getFileNames          8.217  0.080   8.297
changeTimeLimits      8.088  0.127   8.216
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00check.log’
for details.


Installation output

ptairMS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ptairMS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘ptairMS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c align.cpp -o align.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c findEqualGreaterM.cpp -o findEqualGreaterM.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-ptairMS/00new/ptairMS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** testing if installed package keeps a record of temporary installation path
* DONE (ptairMS)

Tests output

ptairMS.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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.

> library(testthat)
> library(ptairMS)
Warning message:
replacing previous import 'Biobase::cache' by 'bit64::cache' when loading 'ptairMS' 
> 
> test_check("ptairMS")
Control1.h5 : 3 peaks detected 
Control2.h5 : 3 peaks detected 
Specie-a1.h5 : 2 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 2 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 2 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 4 peaks detected 
Control2.h5 : 5 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 4 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
Control1.h5 : 3 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 4 peaks detected 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
> 
> proc.time()
   user  system elapsed 
 71.121   1.111  72.224 

Example timings

ptairMS.Rcheck/ptairMS-Ex.timings

nameusersystemelapsed
LocalMaximaSG0.0250.0010.024
PeakList0.8530.0790.934
RunShinnyApp000
alignSamples14.556 0.33214.899
annotation13.046 0.28113.327
calibration0.7020.0040.706
changeTimeLimits8.0880.1278.216
convert_to_mzML11.937 0.44912.385
createPtrSet8.2080.1118.333
defineKnots9.6890.1289.818
detectPeak79.932 0.54880.482
exportSampleMetada8.9830.1209.103
formula2mass0.0000.0030.003
getDirectory8.5350.0728.607
getFileNames8.2170.0808.297
getPeakList13.466 0.13613.603
getSampleMetadata9.0540.1049.158
importSampleMetadata9.0060.0809.087
impute14.273 0.14414.419
imputeMat14.073 0.11214.184
plot11.112 0.05611.169
plotCalib8.7270.0758.803
plotFeatures10.253 0.08010.333
plotRaw10.281 0.10410.385
plotTIC11.175 0.10011.274
readRaw0.1210.0040.126
resetSampleMetadata9.2500.0849.335
rmPeakList9.1990.0849.282
setSampleMetadata 9.949 0.08010.030
timeLimits1.0110.0001.011
updatePtrSet9.050.089.13
writeEset15.075 0.12015.195