Vlad Petyuk
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MSnID |
| Branch: RELEASE_3_6 |
| Last Commit: a8822b3 |
| Last Changed Date: 2017-11-24 13:47:56 -0400 (Fri, 24 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:24:59 -0400 (Thu, 12 Apr 2018).
| Package 904/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSnID 1.12.1 Vlad Petyuk
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: MSnID |
| Version: 1.12.1 |
| Command: rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.12.1.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.12.1.tar.gz |
| StartedAt: 2018-04-12 01:40:13 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:45:47 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 334.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSnID.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.12.1.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.12.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MSnID.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.12.1'
* 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-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:65: missing file link 'R.cache'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:81: missing file link 'R.cache'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:102: missing file link 'proteins'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:188: missing file link 'MSnSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnIDFilter-class.Rd:86: missing file link 'MSnSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/apply_filter.Rd:20: missing file link 'MSnIDFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/optimize_filter.Rd:48: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/optimize_filter.Rd:67: missing file link 'R.cache'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/read_mzIDs.Rd:11: missing file link 'R.cache'
See 'C:/Users/biocbuild/bbs-3.6-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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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 1.49 0.2 7.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
optimize_filter 1.37 0.13 7.63
* 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-3.6-bioc/meat/MSnID.Rcheck/00check.log'
for details.
MSnID.Rcheck/00install.out
install for i386
* installing *source* package 'MSnID' ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:65: missing file link 'R.cache'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:81: missing file link 'R.cache'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:102: missing file link 'proteins'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnID-class.Rd:188: missing file link 'MSnSet'
MSnID-package html
MSnIDFilter-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/MSnIDFilter-class.Rd:86: missing file link 'MSnSet'
accessions html
apply_filter html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/apply_filter.Rd:20: missing file link 'MSnIDFilter'
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-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/optimize_filter.Rd:48: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/optimize_filter.Rd:67: missing file link 'R.cache'
peptides html
psms html
read_mzIDs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp4KaIWN/R.INSTALL3540383c36e4/MSnID/man/read_mzIDs.Rd:11: missing file link 'R.cache'
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_1.12.1.zip
* DONE (MSnID)
In R CMD INSTALL
In R CMD INSTALL
|
MSnID.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 -- Thu Apr 12 01:44:41 2018
***********************************************
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
37.78 0.70 45.86
|
MSnID.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 -- Thu Apr 12 01:45:39 2018
***********************************************
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
44.35 0.71 57.54
|
|
MSnID.Rcheck/examples_i386/MSnID-Ex.timings
|
MSnID.Rcheck/examples_x64/MSnID-Ex.timings
|