| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:40 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the MSstatsPTM package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1272/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 2.1.0 (landing page) Devon Kohler
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: MSstatsPTM |
| Version: 2.1.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MSstatsPTM_2.1.0.tar.gz |
| StartedAt: 2022-12-29 01:41:19 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:44:20 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 181.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsPTM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MSstatsPTM_2.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MSstatsPTM.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsPTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsPTM' version '2.1.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 ... NOTE
Unexported objects imported by ':::' calls:
'MSstats:::.getMedianSigmaSubject' 'MSstats:::.getVarComponent'
See the note in ?`:::` about the use of this operator.
* 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'
.pivotPS: no visible binding for global variable '..keep_cols'
.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'
PStoMSstatsPTMFormat: no visible binding for global variable
'Intensity'
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 ..keep_cols ABUNDANCE
GLOBALPROTEIN Intensity 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 'F:/biocbuild/bbs-3.17-bioc/R/library/MSstatsPTM/libs/x64/MSstatsPTM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 10.84 0.30 11.24
designSampleSizePTM 5.13 0.07 5.21
* 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: 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MSstatsPTM.Rcheck/00check.log'
for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'MSstatsPTM' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++11 -shared -s -static-libgcc -o MSstatsPTM.dll tmp.def RcppExports.o model_adjustment.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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 ** 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)
MSstatsPTM.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 [0;32mOK[0m
test_dataSummarizationPTM.R... 2 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 3 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 4 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 5 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 6 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 7 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 8 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 9 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 10 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 11 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 12 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 13 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 14 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 15 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 16 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 17 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 18 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 19 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 20 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 21 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 22 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 23 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 24 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 25 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 26 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 27 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 28 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 29 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 30 tests [0;32mOK[0m Starting PTM summarization...
test_dataSummarizationPTM.R... 31 tests [0;32mOK[0m [0;34m0.3s[0m
test_dataSummarizationPTM_TMT.R 0 tests
test_dataSummarizationPTM_TMT.R 1 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 2 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 3 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 4 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 5 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 6 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 7 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 8 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 9 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 10 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 11 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 12 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 13 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 14 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 15 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 16 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 17 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 18 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 19 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 20 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 21 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 22 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 23 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 24 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 25 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 26 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 27 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 28 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 29 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 30 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 31 tests [0;32mOK[0m [0;34m0.3s[0m
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 1 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 2 tests [0;32mOK[0m Starting PTM modeling...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m Starting PTM modeling...
INFO [2022-12-29 01:43:58] == Start to test and get inference in whole plot ...
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INFO [2022-12-29 01:44:02] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2022-12-29 01:44:02] == Start to test and get inference in whole plot ...
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INFO [2022-12-29 01:44:02] == Comparisons for all proteins are done.
Starting adjustment...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 4 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 5 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 6 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 7 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 8 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 9 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m Starting PTM modeling...
INFO [2022-12-29 01:44:03] Design: 2 mixtures.
INFO [2022-12-29 01:44:03] Design: 1 MS run per mixture.
INFO [2022-12-29 01:44:03] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2022-12-29 01:44:03] Model fitting for 90 proteins.
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INFO [2022-12-29 01:44:04] Testing for 90 proteins:
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Starting Protein modeling...
INFO [2022-12-29 01:44:05] Design: 2 mixtures.
INFO [2022-12-29 01:44:05] Design: 1 MS run per mixture.
INFO [2022-12-29 01:44:05] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2022-12-29 01:44:05] Model fitting for 85 proteins.
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INFO [2022-12-29 01:44:09] Testing for 85 proteins:
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Starting adjustment...
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 11 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 12 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 13 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 14 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 15 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 16 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 17 tests [0;32mOK[0m [0;34m14.9s[0m
All ok, 79 results (15.4s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
19.73 0.92 20.70
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| MSstatsPTMSiteLocator | 0 | 0 | 0 | |
| MaxQtoMSstatsPTMFormat | 0.03 | 0.00 | 0.03 | |
| PStoMSstatsPTMFormat | 0.08 | 0.00 | 0.08 | |
| ProgenesistoMSstatsPTMFormat | 0.08 | 0.00 | 0.07 | |
| SkylinetoMSstatsPTMFormat | 0.04 | 0.00 | 0.05 | |
| SpectronauttoMSstatsPTMFormat | 0.07 | 0.00 | 0.06 | |
| annotSite | 0 | 0 | 0 | |
| dataProcessPlotsPTM | 2.32 | 0.05 | 2.39 | |
| dataSummarizationPTM | 1.91 | 0.03 | 1.96 | |
| dataSummarizationPTM_TMT | 3.34 | 0.15 | 3.57 | |
| designSampleSizePTM | 5.13 | 0.07 | 5.21 | |
| groupComparisonPTM | 4.03 | 0.16 | 4.19 | |
| groupComparisonPlotsPTM | 10.84 | 0.30 | 11.24 | |
| locateMod | 0 | 0 | 0 | |
| locatePTM | 0.04 | 0.00 | 0.03 | |
| raw.input | 0.04 | 0.00 | 0.04 | |
| raw.input.tmt | 0 | 0 | 0 | |
| summary.data | 0.46 | 0.27 | 0.72 | |
| summary.data.tmt | 1.01 | 0.51 | 1.56 | |
| tidyFasta | 0 | 0 | 0 | |