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CHECK report for MSnID on tokay2

This page was generated on 2019-10-16 12:31:10 -0400 (Wed, 16 Oct 2019).

Package 1056/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.18.1
Vlad Petyuk
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MSnID
Branch: RELEASE_3_9
Last Commit: d328143
Last Changed Date: 2019-07-03 03:08:09 -0400 (Wed, 03 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.18.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSnID_1.18.1.tar.gz
StartedAt: 2019-10-16 05:26:13 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:32:39 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 385.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MSnID.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MSnID_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MSnID.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.18.1'
* 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 'MSnID' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/MSnID/man/read_mzIDs.Rd:27: missing file link 'mzR-package'
See 'C:/Users/biocbuild/bbs-3.9-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 : : 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'
infer_parsimonious_accessions,MSnID: no visible binding for global
  variable 'accession'
infer_parsimonious_accessions,MSnID: no visible binding for global
  variable 'pepSeq'
infer_parsimonious_accessions,MSnID: no visible global function
  definition for '.'
infer_parsimonious_accessions,MSnID: no visible binding for global
  variable 'num'
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 num 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 ... WARNING
Missing link or links in documentation object 'read_mzIDs.Rd':
  '[mzR]{mzR-package}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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
infer_parsimonious_accessions 2.99   2.02    4.25
optimize_filter               1.95   0.48    8.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
optimize_filter 1.95   0.33    8.28
* 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MSnID_1.18.1.tar.gz && rm -rf MSnID.buildbin-libdir && mkdir MSnID.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnID.buildbin-libdir MSnID_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MSnID_1.18.1.zip && rm MSnID_1.18.1.tar.gz MSnID_1.18.1.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 2559k  100 2559k    0     0  28.1M      0 --:--:-- --:--:-- --:--:-- 30.8M

install for i386

* installing *source* package 'MSnID' ...
** using staged installation
** 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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/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
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpw1V6de/R.INSTALL1ac876b47a23/MSnID/man/read_mzIDs.Rd:27: missing file link 'mzR-package'
    recalibrate                             html  
** 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

install for x64

* installing *source* package 'MSnID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.18.1.zip
* DONE (MSnID)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MSnID' successfully unpacked and MD5 sums checked

Tests output

MSnID.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 05:30:12 2019 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  44.67    5.51   58.43

MSnID.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 05:31:59 2019 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  46.26    5.14  105.81

Example timings

MSnID.Rcheck/examples_i386/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.190.120.39
accessions0.220.000.22
apply_filter0.760.180.97
assess_missed_cleavages0.240.030.26
assess_termini0.200.040.25
correct_peak_selection0.120.000.13
data0.080.160.26
evaluate_filter0.410.090.60
id_quality0.170.030.23
infer_parsimonious_accessions2.992.024.25
mass_measurement_error0.160.000.15
optimize_filter1.950.488.85
peptides0.090.000.10
psms0.080.040.10
read_mzIDs000
recalibrate0.110.000.11

MSnID.Rcheck/examples_x64/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.150.070.34
accessions0.590.000.59
apply_filter0.420.150.74
assess_missed_cleavages0.250.000.25
assess_termini0.220.000.24
correct_peak_selection0.410.010.44
data0.110.070.25
evaluate_filter0.300.040.45
id_quality0.170.040.22
infer_parsimonious_accessions2.441.323.44
mass_measurement_error0.110.020.13
optimize_filter1.950.338.28
peptides0.080.030.11
psms0.130.000.12
read_mzIDs000
recalibrate0.110.000.11