Vlad Petyuk
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/MSnID |
| Branch: RELEASE_3_11 |
| Last Commit: 56cf547 |
| Last Changed Date: 2020-04-27 14:43:17 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:13 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE MSnID PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1142/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSnID 1.22.0 Vlad Petyuk
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: MSnID |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MSnID_1.22.0.tar.gz |
| StartedAt: 2020-10-17 06:17:08 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:22:55 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 346.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSnID.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MSnID_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MSnID.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.22.0'
* 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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/MSnID/man/read_mzIDs.Rd:27: missing file link 'mzR-package'
See 'C:/Users/biocbuild/bbs-3.11-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 ... 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 (user + system) or elapsed time > 5s
user system elapsed
optimize_filter 2.5 0.51 10.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
optimize_filter 2.7 0.45 12.6
* 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-3.11-bioc/meat/MSnID.Rcheck/00check.log'
for details.
MSnID.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MSnID_1.22.0.tar.gz && rm -rf MSnID.buildbin-libdir && mkdir MSnID.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnID.buildbin-libdir MSnID_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MSnID_1.22.0.zip && rm MSnID_1.22.0.tar.gz MSnID_1.22.0.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
20 2558k 20 512k 0 0 2596k 0 --:--:-- --:--:-- --:--:-- 2680k
100 2558k 100 2558k 0 0 6024k 0 --:--:-- --:--:-- --:--:-- 6121k
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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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-3.11-bioc/tmpdir/RtmpGKN3GV/R.INSTALL25dc52991673/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_1.22.0.zip
* DONE (MSnID)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MSnID' successfully unpacked and MD5 sums checked
|
MSnID.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.
> 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 Oct 17 06:21:48 2020
***********************************************
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
39.95 4.51 49.79
|
MSnID.Rcheck/tests_x64/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.
> 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 Oct 17 06:22:46 2020
***********************************************
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
44.98 2.79 57.32
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MSnID.Rcheck/examples_i386/MSnID-Ex.timings
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MSnID.Rcheck/examples_x64/MSnID-Ex.timings
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