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CHECK report for MSnID on tokay1

This page was generated on 2019-04-13 11:24:21 -0400 (Sat, 13 Apr 2019).

Package 1011/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.16.1
Vlad Petyuk
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MSnID
Branch: RELEASE_3_8
Last Commit: 98a3641
Last Changed Date: 2018-11-30 14:22:23 -0400 (Fri, 30 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.16.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MSnID_1.16.1.tar.gz
StartedAt: 2019-04-13 04:01:24 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:06:46 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 322.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MSnID.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MSnID_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSnID.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSnID' version '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'MSnID' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:65: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:81: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:102: file link 'proteins' in package 'MSnID' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:188: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnIDFilter-class.Rd:86: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/apply_filter.Rd:20: file link 'MSnIDFilter' in package 'MSnID' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/optimize_filter.Rd:48: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/optimize_filter.Rd:67: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/read_mzIDs.Rd:11: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSnID.Rcheck/00install.out' for details.
* 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 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 ... NOTE
.construct_optimization_grid : <anonymous>: no visible global function
  definition for 'quantile'
.get_num_pep_for_fdr: no visible global function definition for 'rnorm'
.optimize_filter: no visible global function definition for 'optim'
.read_mzIDs.mzR: no visible binding for global variable 'i'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'spectrumID'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'name'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'mass'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'location'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'modification'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'DatabaseAccess'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'DatabaseDescription'
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'DBseqLength'
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable 'accession'
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable 'N'
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable 'pepSeq'
recalibrate,MSnID: no visible global function definition for 'median'
recalibrate,MSnID: no visible global function definition for 'density'
Undefined global functions or variables:
  DBseqLength DatabaseAccess DatabaseDescription N accession density i
  location mass median modification name optim pepSeq quantile rnorm
  spectrumID
Consider adding
  importFrom("stats", "density", "median", "optim", "quantile", "rnorm")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
optimize_filter 1.97   0.36     7.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
optimize_filter 1.87   0.21    6.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSnID.Rcheck/00check.log'
for details.

Installation output

MSnID.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MSnID_1.16.1.tar.gz && rm -rf MSnID.buildbin-libdir && mkdir MSnID.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnID.buildbin-libdir MSnID_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MSnID_1.16.1.zip && rm MSnID_1.16.1.tar.gz MSnID_1.16.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2560k  100 2560k    0     0  24.0M      0 --:--:-- --:--:-- --:--:-- 25.0M

install for i386

* installing *source* package 'MSnID' ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSnID'
    finding HTML links ... done
    MSnID-class                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:65: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:81: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:102: file link 'proteins' in package 'MSnID' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnID-class.Rd:188: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
    MSnID-package                           html  
    MSnIDFilter-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/MSnIDFilter-class.Rd:86: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
    accessions                              html  
    apply_filter                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/apply_filter.Rd:20: file link 'MSnIDFilter' in package 'MSnID' does not exist and so has been treated as a topic
    assess_missed_cleavages                 html  
    assess_termini                          html  
    correct_peak_selection                  html  
    data                                    html  
    evaluate_filter                         html  
    id_quality                              html  
    infer_parsimonious_accessions           html  
    mass_measurement_error                  html  
    optimize_filter                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/optimize_filter.Rd:48: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/optimize_filter.Rd:67: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
    peptides                                html  
    psms                                    html  
    read_mzIDs                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYR3mMf/R.INSTALL22d860fd905/MSnID/man/read_mzIDs.Rd:11: file link 'R.cache' in package 'R.cache' does not exist and so has been treated as a topic
    recalibrate                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MSnID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.16.1.zip
* DONE (MSnID)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MSnID' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MSnID.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...



RUNIT TEST PROTOCOL -- Sat Apr 13 04:05:48 2019 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  32.06    3.87   39.48

MSnID.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...



RUNIT TEST PROTOCOL -- Sat Apr 13 04:06:42 2019 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  37.17    3.35   53.78

Example timings

MSnID.Rcheck/examples_i386/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.150.120.27
accessions0.110.000.11
apply_filter0.700.130.84
assess_missed_cleavages0.180.010.19
assess_termini0.170.030.21
correct_peak_selection0.110.000.11
data0.110.160.23
evaluate_filter0.610.090.67
id_quality0.090.030.14
infer_parsimonious_accessions2.521.572.91
mass_measurement_error0.080.010.10
optimize_filter1.970.367.30
peptides0.090.000.09
psms0.110.000.11
read_mzIDs000
recalibrate0.110.020.12

MSnID.Rcheck/examples_x64/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.190.110.25
accessions0.190.040.22
apply_filter0.620.100.73
assess_missed_cleavages0.180.040.20
assess_termini0.180.030.22
correct_peak_selection0.520.010.53
data0.150.080.21
evaluate_filter0.190.090.31
id_quality0.080.000.12
infer_parsimonious_accessions1.701.332.36
mass_measurement_error0.10.00.1
optimize_filter1.870.216.83
peptides0.080.000.07
psms0.080.000.08
read_mzIDs000
recalibrate0.090.010.11