Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-25 11:07:47 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MSstatsPTM on riesling1


To the developers/maintainers of the MSstatsPTM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1226/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 1.5.2  (landing page)
Devon Kohler
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: master
git_last_commit: e2ca4fa
git_last_commit_date: 2021-12-21 10:38:27 -0500 (Tue, 21 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'MSstatsTMT' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'MSstatsTMT' which is not available

Summary

Package: MSstatsPTM
Version: 1.5.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSstatsPTM_1.5.2.tar.gz
StartedAt: 2022-01-24 19:28:59 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 19:31:51 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 171.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSstatsPTM_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MSstatsPTM.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsPTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsPTM' version '1.5.2'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MSstatsPTM' can be installed ... OK
* 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
* 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
.format.data.process.plots: no visible binding for global variable
  'ABUNDANCE'
.plot.model.volcano: no visible binding for global variable
  'text.angle'
.progensis.add.sites: no visible binding for global variable
  '..col_order'
.qc.all.plot.lf: no visible binding for global variable 'text.angle'
.qc.single.plot.lf: no visible binding for global variable 'text.angle'
.rmConfounded: no visible binding for global variable '..col_res'
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  'PeptideSequence'
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
  'Type'
SpectronauttoMSstatsPTMFormat: no visible binding for global variable
  'R.Condition'
SpectronauttoMSstatsPTMFormat: no visible binding for global variable
  'join_PeptideSequence'
SpectronauttoMSstatsPTMFormat: no visible binding for global variable
  'PeptideSequence'
dataProcessPlotsPTM: no visible binding for global variable
  'PROTEINNAME'
dataProcessPlotsPTM: no visible binding for global variable
  'GLOBALPROTEIN'
dataSummarizationPTM: no visible binding for global variable 'address'
locatePTM: no visible binding for global variable '..col_seq'
locatePTM: no visible binding for global variable '..col_fasta'
Undefined global functions or variables:
  ..col_fasta ..col_order ..col_res ..col_seq ABUNDANCE GLOBALPROTEIN
  PROTEINNAME PeptideSequence R.Condition Type address
  join_PeptideSequence text.angle
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/MSstatsPTM/libs/x64/MSstatsPTM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
groupComparisonPlotsPTM 12.86    0.1   12.97
groupComparisonPTM       5.42    0.1    5.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/MSstatsPTM.Rcheck/00check.log'
for details.



Installation output

MSstatsPTM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MSstatsPTM
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MSstatsPTM' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c model_adjustment.cpp -o model_adjustment.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MSstatsPTM.dll tmp.def RcppExports.o model_adjustment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstatsPTM'
    finding HTML links ... done
    MSstatsPTM                              html  
    MaxQtoMSstatsPTMFormat                  html  
    ProgenesistoMSstatsPTMFormat            html  
    SpectronauttoMSstatsPTMFormat           html  
    annotSite                               html  
    dataProcessPlotsPTM                     html  
    dataSummarizationPTM                    html  
    dataSummarizationPTM_TMT                html  
    groupComparisonPTM                      html  
    groupComparisonPlotsPTM                 html  
    locateMod                               html  
    locatePTM                               html  
    raw.input                               html  
    raw.input.tmt                           html  
    summary.data                            html  
    summary.data.tmt                        html  
    tidyFasta                               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
* DONE (MSstatsPTM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'GeneRegionScan' is missing or broken
 done

Tests output

MSstatsPTM.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.

> 
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+   tinytest::test_package("MSstatsPTM")
+ }

test_dataSummarizationPTM.R...    0 tests    
test_dataSummarizationPTM.R...    1 tests OK 
test_dataSummarizationPTM.R...    2 tests OK 
test_dataSummarizationPTM.R...    3 tests OK 
test_dataSummarizationPTM.R...    4 tests OK 
test_dataSummarizationPTM.R...    5 tests OK 
test_dataSummarizationPTM.R...    6 tests OK 
test_dataSummarizationPTM.R...    7 tests OK 
test_dataSummarizationPTM.R...    8 tests OK 
test_dataSummarizationPTM.R...    9 tests OK 
test_dataSummarizationPTM.R...   10 tests OK 
test_dataSummarizationPTM.R...   11 tests OK 
test_dataSummarizationPTM.R...   12 tests OK 
test_dataSummarizationPTM.R...   13 tests OK 
test_dataSummarizationPTM.R...   14 tests OK 
test_dataSummarizationPTM.R...   15 tests OK 
test_dataSummarizationPTM.R...   16 tests OK 
test_dataSummarizationPTM.R...   17 tests OK 
test_dataSummarizationPTM.R...   18 tests OK 
test_dataSummarizationPTM.R...   19 tests OK 
test_dataSummarizationPTM.R...   20 tests OK 
test_dataSummarizationPTM.R...   21 tests OK 
test_dataSummarizationPTM.R...   22 tests OK 
test_dataSummarizationPTM.R...   23 tests OK 
test_dataSummarizationPTM.R...   24 tests OK 
test_dataSummarizationPTM.R...   25 tests OK 
test_dataSummarizationPTM.R...   26 tests OK 
test_dataSummarizationPTM.R...   27 tests OK 
test_dataSummarizationPTM.R...   28 tests OK 
test_dataSummarizationPTM.R...   29 tests OK 
test_dataSummarizationPTM.R...   30 tests OK Starting PTM summarization...

test_dataSummarizationPTM.R...   31 tests OK 0.2s

test_dataSummarizationPTM_TMT.R    0 tests    
test_dataSummarizationPTM_TMT.R    1 tests OK 
test_dataSummarizationPTM_TMT.R    2 tests OK 
test_dataSummarizationPTM_TMT.R    3 tests OK 
test_dataSummarizationPTM_TMT.R    4 tests OK 
test_dataSummarizationPTM_TMT.R    5 tests OK 
test_dataSummarizationPTM_TMT.R    6 tests OK 
test_dataSummarizationPTM_TMT.R    7 tests OK 
test_dataSummarizationPTM_TMT.R    8 tests OK 
test_dataSummarizationPTM_TMT.R    9 tests OK 
test_dataSummarizationPTM_TMT.R   10 tests OK 
test_dataSummarizationPTM_TMT.R   11 tests OK 
test_dataSummarizationPTM_TMT.R   12 tests OK 
test_dataSummarizationPTM_TMT.R   13 tests OK 
test_dataSummarizationPTM_TMT.R   14 tests OK 
test_dataSummarizationPTM_TMT.R   15 tests OK 
test_dataSummarizationPTM_TMT.R   16 tests OK 
test_dataSummarizationPTM_TMT.R   17 tests OK 
test_dataSummarizationPTM_TMT.R   18 tests OK 
test_dataSummarizationPTM_TMT.R   19 tests OK 
test_dataSummarizationPTM_TMT.R   20 tests OK 
test_dataSummarizationPTM_TMT.R   21 tests OK 
test_dataSummarizationPTM_TMT.R   22 tests OK 
test_dataSummarizationPTM_TMT.R   23 tests OK 
test_dataSummarizationPTM_TMT.R   24 tests OK 
test_dataSummarizationPTM_TMT.R   25 tests OK 
test_dataSummarizationPTM_TMT.R   26 tests OK 
test_dataSummarizationPTM_TMT.R   27 tests OK 
test_dataSummarizationPTM_TMT.R   28 tests OK 
test_dataSummarizationPTM_TMT.R   29 tests OK 
test_dataSummarizationPTM_TMT.R   30 tests OK 
test_dataSummarizationPTM_TMT.R   31 tests OK 0.2s

test_groupComparisonPTM.R.....    0 tests    
test_groupComparisonPTM.R.....    0 tests    
test_groupComparisonPTM.R.....    1 tests OK 
test_groupComparisonPTM.R.....    2 tests OK Starting PTM modeling...

test_groupComparisonPTM.R.....    3 tests OK Starting PTM modeling...
INFO  [2022-01-24 19:31:30]  == Start to test and get inference in whole plot ...

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INFO  [2022-01-24 19:31:34]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2022-01-24 19:31:34]  == Start to test and get inference in whole plot ...

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INFO  [2022-01-24 19:31:34]  == Comparisons for all proteins are done.
Starting adjustment...

test_groupComparisonPTM.R.....    3 tests OK 
test_groupComparisonPTM.R.....    4 tests OK 
test_groupComparisonPTM.R.....    5 tests OK 
test_groupComparisonPTM.R.....    6 tests OK 
test_groupComparisonPTM.R.....    7 tests OK 
test_groupComparisonPTM.R.....    8 tests OK 
test_groupComparisonPTM.R.....    9 tests OK 
test_groupComparisonPTM.R.....   10 tests OK Starting PTM modeling...
INFO  [2022-01-24 19:31:34] Design: 2 mixtures.
INFO  [2022-01-24 19:31:34] Design: 1 MS run per mixture.
INFO  [2022-01-24 19:31:34] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2022-01-24 19:31:34] Model fitting for 90 proteins.

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INFO  [2022-01-24 19:31:36] Testing for 90 proteins:

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Starting Protein modeling...
INFO  [2022-01-24 19:31:36] Design: 2 mixtures.
INFO  [2022-01-24 19:31:36] Design: 1 MS run per mixture.
INFO  [2022-01-24 19:31:36] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2022-01-24 19:31:36] Model fitting for 85 proteins.

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INFO  [2022-01-24 19:31:41] Testing for 85 proteins:

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Starting adjustment...

test_groupComparisonPTM.R.....   10 tests OK 
test_groupComparisonPTM.R.....   11 tests OK 
test_groupComparisonPTM.R.....   12 tests OK 
test_groupComparisonPTM.R.....   13 tests OK 
test_groupComparisonPTM.R.....   14 tests OK 
test_groupComparisonPTM.R.....   15 tests OK 
test_groupComparisonPTM.R.....   16 tests OK 
test_groupComparisonPTM.R.....   17 tests OK 14.5s
All ok, 79 results (14.9s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  19.20    0.89   20.10 

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsPTMFormat0.050.000.04
ProgenesistoMSstatsPTMFormat0.070.000.08
SpectronauttoMSstatsPTMFormat0.030.000.03
annotSite000
dataProcessPlotsPTM1.860.041.90
dataSummarizationPTM1.840.031.88
dataSummarizationPTM_TMT3.800.284.06
groupComparisonPTM5.420.105.53
groupComparisonPlotsPTM12.86 0.1012.97
locateMod000
locatePTM0.030.000.03
raw.input0.050.000.05
raw.input.tmt000
summary.data0.30.20.5
summary.data.tmt0.510.380.89
tidyFasta0.020.000.01