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CHECK report for pRolocdata on riesling1

This page was generated on 2021-01-14 15:59:10 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE pRolocdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 272/385HostnameOS / ArchINSTALLBUILDCHECK
pRolocdata 1.29.0
Laurent Gatto
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/pRolocdata
Branch: master
Last Commit: 43ec622
Last Changed Date: 2020-10-27 10:00:16 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: pRolocdata
Version: 1.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRolocdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pRolocdata_1.29.0.tar.gz
StartedAt: 2021-01-14 11:34:10 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:39:39 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 328.4 seconds
RetCode: 0
Status:  OK  
CheckDir: pRolocdata.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRolocdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pRolocdata_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/pRolocdata.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pRolocdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pRolocdata' version '1.29.0'
* 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 'pRolocdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 304.6Mb
  sub-directories of 1Mb or more:
    data      70.3Mb
    extdata  233.4Mb
* checking package 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
krahmer2018pcp 7.36    0.3    7.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
krahmer2018pcp 7.89   0.23    8.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/pRolocdata.Rcheck/00check.log'
for details.



Installation output

pRolocdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/pRolocdata_1.29.0.tar.gz && rm -rf pRolocdata.buildbin-libdir && mkdir pRolocdata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pRolocdata.buildbin-libdir pRolocdata_1.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pRolocdata_1.29.0.zip && rm pRolocdata_1.29.0.tar.gz pRolocdata_1.29.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 14  245M   14 35.9M    0     0  49.8M      0  0:00:04 --:--:--  0:00:04 49.8M
 44  245M   44  109M    0     0  63.5M      0  0:00:03  0:00:01  0:00:02 63.4M
 81  245M   81  199M    0     0  73.2M      0  0:00:03  0:00:02  0:00:01 73.1M
100  245M  100  245M    0     0  73.8M      0  0:00:03  0:00:03 --:--:-- 73.8M

install for i386

* installing *source* package 'pRolocdata' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pRolocdata'
    finding HTML links ... done
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** building package indices
** 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

install for x64

* installing *source* package 'pRolocdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pRolocdata' as pRolocdata_1.29.0.zip
* DONE (pRolocdata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'pRolocdata' successfully unpacked and MD5 sums checked

Tests output

pRolocdata.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.17.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

> library(pRolocdata)

This is pRolocdata version 1.29.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
  13.07    0.56   13.62 

pRolocdata.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.17.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

> library(pRolocdata)

This is pRolocdata version 1.29.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRolocdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
  11.53    0.81   12.35 

Example timings

pRolocdata.Rcheck/examples_i386/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.050.000.05
Shin20202.750.214.66
ToxoLopit0.440.030.49
andreyev20100.550.010.56
andy20110.060.000.06
at_chloro0.060.040.10
baers20180.300.030.32
beltran20160.480.030.51
davies20180.280.000.28
dunkley20060.010.000.02
fabre20150.220.030.25
foster20060.030.000.03
groen20141.140.031.18
hall20090.160.000.15
havugimana20120.080.000.08
hirst20180.390.020.40
hyperLOPIT20152.920.062.99
hyperLOPITU2OS20171.170.081.31
itzhak20160.550.000.57
itzhak20171.520.001.52
itzhak2017dynamic1.140.041.19
kirkwood20130.030.000.03
kozik20200.190.000.20
krahmer2018pcp7.360.307.65
kristensen20120.020.000.01
lopimsSyn20.890.060.96
mulvey20151.790.001.81
nikolovski20120.250.010.27
nikolovski20140.280.050.32
orre20190.350.050.39
pRolocdata0.010.000.02
pRolocmetadata0.000.010.01
rodriguez2012r10.600.020.61
stekhoven20140.180.000.17
tan20090.010.000.02
trotter20100.200.030.25
yeast0.270.030.32

pRolocdata.Rcheck/examples_x64/pRolocdata-Ex.timings

nameusersystemelapsed
E14TG2a0.030.000.03
Shin20203.110.154.93
ToxoLopit0.820.040.84
andreyev20100.470.010.48
andy20110.050.000.05
at_chloro0.060.000.06
baers20180.310.000.32
beltran20160.460.020.50
davies20180.210.030.25
dunkley20060.000.010.02
fabre20150.210.020.24
foster20060.030.000.03
groen20140.730.060.80
hall20090.140.000.14
havugimana20120.090.020.11
hirst20180.740.040.78
hyperLOPIT20152.440.042.47
hyperLOPITU2OS20171.150.031.27
itzhak20160.490.040.55
itzhak20171.760.051.81
itzhak2017dynamic1.110.021.13
kirkwood20130.030.000.03
kozik20200.140.030.19
krahmer2018pcp7.890.238.13
kristensen20120.020.000.02
lopimsSyn20.530.030.56
mulvey20151.780.051.82
nikolovski20120.200.060.27
nikolovski20140.290.010.31
orre20190.320.040.36
pRolocdata0.020.000.02
pRolocmetadata0.020.000.02
rodriguez2012r10.570.000.58
stekhoven20140.180.000.17
tan20090.010.000.02
trotter20100.270.000.28
yeast0.280.030.33