Mateusz Staniak
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MSstatsBig |
| git_branch: RELEASE_3_20 |
| git_last_commit: 336b43b |
| git_last_commit_date: 2024-10-29 11:24:58 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 | ||||
| Package 1351/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsBig 1.4.0 (landing page) Mateusz Staniak
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the MSstatsBig package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsBig.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MSstatsBig |
| Version: 1.4.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsBig.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSstatsBig_1.4.0.tar.gz |
| StartedAt: 2024-12-20 03:52:05 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:53:36 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 91.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsBig.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsBig.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSstatsBig_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsBig.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsBig/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsBig' version '1.4.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MSstatsBig' 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 code 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
MSstatsPreprocessBig: no visible binding for global variable 'input'
MSstatsPreprocessBigArrow: no visible binding for global variable
'PeptideSequence'
MSstatsPreprocessBigArrow: no visible binding for global variable
'PrecursorCharge'
MSstatsPreprocessBigArrow: no visible binding for global variable
'FragmentIon'
MSstatsPreprocessBigArrow: no visible binding for global variable
'ProductCharge'
MSstatsPreprocessBigArrow: no visible binding for global variable
'ProteinName'
MSstatsPreprocessBigArrow: no visible binding for global variable
'Feature'
MSstatsPreprocessBigArrow: no visible binding for global variable
'Intensity'
MSstatsPreprocessBigArrow: no visible binding for global variable
'MeanAbundance'
MSstatsPreprocessBigArrow: no visible binding for global variable
'feature_rank'
MSstatsPreprocessBigArrow: no visible binding for global variable
'NumProteins'
MSstatsPreprocessBigArrow: no visible binding for global variable
'IsotopeLabelType'
MSstatsPreprocessBigArrow: no visible binding for global variable 'Run'
MSstatsPreprocessBigArrow: no visible binding for global variable
'Condition'
MSstatsPreprocessBigArrow: no visible binding for global variable
'BioReplicate'
MSstatsPreprocessBigArrow: no visible binding for global variable
'NumObs'
MSstatsPreprocessBigSparklyr: no visible global function definition for
'%>%'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'Condition'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'BioReplicate'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'PeptideSequence'
MSstatsPreprocessBigSparklyr: no visible global function definition for
'n_distinct'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'ProteinName'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'NumProteins'
MSstatsPreprocessBigSparklyr: no visible global function definition for
'tbl'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'PrecursorCharge'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'FragmentIon'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'ProductCharge'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'IsotopeLabelType'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'Run'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'Intensity'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'NumObs'
MSstatsPreprocessBigSparklyr: no visible global function definition for
'min_rank'
MSstatsPreprocessBigSparklyr: no visible binding for global variable
'Rank'
cleanSpectronautChunk: no visible global function definition for
'all_of'
cleanSpectronautChunk: no visible binding for global variable
'Intensity'
cleanSpectronautChunk: no visible binding for global variable
'Excluded'
cleanSpectronautChunk: no visible binding for global variable
'Identified'
cleanSpectronautChunk: no visible binding for global variable
'EGQvalue'
cleanSpectronautChunk: no visible binding for global variable
'PGQvalue'
cleanSpectronautChunk: no visible binding for global variable
'FFrgLossType'
cleanSpectronautChunk: no visible binding for global variable
'LabeledSequence'
cleanSpectronautChunk: no visible global function definition for ':='
cleanSpectronautChunk: no visible binding for global variable
'IsotopeLabelType'
cleanSpectronautChunk: no visible binding for global variable
'IsLabeled'
cleanSpectronautChunk: no visible binding for global variable
'ProteinName'
cleanSpectronautChunk: no visible binding for global variable
'PeptideSequence'
cleanSpectronautChunk: no visible binding for global variable
'PrecursorCharge'
cleanSpectronautChunk: no visible binding for global variable
'FragmentIon'
cleanSpectronautChunk: no visible binding for global variable
'ProductCharge'
cleanSpectronautChunk: no visible binding for global variable 'Run'
cleanSpectronautChunk: no visible binding for global variable
'BioReplicate'
cleanSpectronautChunk: no visible binding for global variable
'Condition'
Undefined global functions or variables:
%>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature
FragmentIon Identified Intensity IsLabeled IsotopeLabelType
LabeledSequence MeanAbundance NumObs NumProteins PGQvalue
PeptideSequence PrecursorCharge ProductCharge ProteinName Rank Run
all_of feature_rank input min_rank n_distinct tbl
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bigSpectronauttoMSstatsFormat 5.39 0.42 5.91
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsBig.Rcheck/00check.log'
for details.
MSstatsBig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MSstatsBig ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MSstatsBig' ... ** using staged installation ** R ** 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 (MSstatsBig)
MSstatsBig.Rcheck/MSstatsBig-Ex.timings
| name | user | system | elapsed | |
| MSstatsAddAnnotationBig | 0.80 | 0.09 | 0.92 | |
| MSstatsPreprocessBig | 0.44 | 0.02 | 0.46 | |
| bigFragPipetoMSstatsFormat | 0.22 | 0.03 | 0.25 | |
| bigSpectronauttoMSstatsFormat | 5.39 | 0.42 | 5.91 | |