Jemma Wu
| Snapshot Date: 2024-11-17 13:40 -0500 (Sun, 17 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/SwathXtend |
| git_branch: devel |
| git_last_commit: 4c2c9ad |
| git_last_commit_date: 2024-10-29 10:08:33 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-18 11:34 -0500 (Mon, 18 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4740 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4454 |
| 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 2078/2268 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SwathXtend 2.29.0 (landing page) Jemma Wu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SwathXtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SwathXtend.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: SwathXtend |
| Version: 2.29.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SwathXtend.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SwathXtend_2.29.0.tar.gz |
| StartedAt: 2024-11-18 05:29:11 -0500 (Mon, 18 Nov 2024) |
| EndedAt: 2024-11-18 05:31:22 -0500 (Mon, 18 Nov 2024) |
| EllapsedTime: 131.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SwathXtend.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SwathXtend.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SwathXtend_2.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SwathXtend.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SwathXtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SwathXtend' version '2.29.0'
* 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 'SwathXtend' can be installed ... OK
* checking installed package size ... INFO
installed size is 351.5Mb
sub-directories of 1Mb or more:
files 351.3Mb
* 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
reliabilityCheckSwath: warning in venn.diagram(list(seedSwath =
ds.seed$Peptide, extSwath = ds.ext$Peptide), file = "venn of
peptide.png", category.names = c("seed", "extended"), fill =
c("aquamarine1", "chartreuse"), main = paste("Peptides at FDR pass",
nfdr)): partial argument match of 'file' to 'filename'
reliabilityCheckSwath: warning in venn.diagram(list(seedSwath =
ds.seed$Protein, extSwath = ds.ext$Protein), file = "venn of
protein.png", category.names = c("seed", "extended"), fill =
c("aquamarine1", "chartreuse"), main = paste("Proteins at FDR pass",
nfdr)): partial argument match of 'file' to 'filename'
alignRTbyHydro: no visible global function definition for 'as.formula'
alignRTbyHydro: no visible global function definition for 'lm'
alignRTbyHydro: no visible global function definition for 'predict'
applyttest : <anonymous>: no visible global function definition for
't.test'
applyttest : <anonymous>: no visible global function definition for
'na.omit'
applyttestPep : <anonymous>: no visible global function definition for
'na.omit'
applyttestPep: no visible global function definition for 'aggregate'
applyttestPep : <anonymous>: no visible global function definition for
't.test'
checkQuality: no visible global function definition for 'median'
computeRIICor : <anonymous>: no visible global function definition for
'cor'
computeRIICor: no visible global function definition for 'data'
computeRIICor: no visible global function definition for 'png'
computeRIICor: no visible global function definition for 'boxplot'
computeRIICor: no visible global function definition for 'abline'
computeRIICor: no visible global function definition for 'dev.off'
computeRTCor: no visible global function definition for 'cor'
computeRTCor: no visible global function definition for 'predict'
computeRTCor: no visible global function definition for 'png'
computeRTCor: no visible global function definition for 'lines'
computeRTCor: no visible global function definition for 'lowess'
computeRTCor: no visible global function definition for 'text'
computeRTCor: no visible global function definition for 'dev.off'
computeRTCor: no visible global function definition for 'abline'
computeRTCor: no visible global function definition for 'axis'
computeRTCor: no visible global function definition for 'as.formula'
computeRTCor: no visible global function definition for 'lm'
computeRTCor: no visible global function definition for 'layout'
computeRTCor: no visible global function definition for 'resid'
computeRTCor: no visible global function definition for 'residuals'
cv: no visible global function definition for 'sd'
cv: no visible global function definition for 'na.omit'
fdr.crit : <anonymous>: no visible global function definition for
'na.omit'
medianNorm : <anonymous>: no visible global function definition for
'median'
medianNorm : <anonymous>: no visible global function definition for
'na.omit'
mlr: no visible global function definition for 'na.omit'
mlr: no visible global function definition for 'hist'
mlr: no visible global function definition for 'density'
mlr: no visible global function definition for 'lines'
mlr: no visible global function definition for 'abline'
mlr: no visible global function definition for 'text'
mlr: no visible global function definition for 'segments'
mlrrep: no visible global function definition for 'na.omit'
normalise: no visible global function definition for 'aggregate'
outputLib: no visible global function definition for 'write.table'
parseAccession: no visible global function definition for 'na.omit'
plotDensities: no visible global function definition for 'rainbow'
plotDensities: no visible global function definition for 'density'
plotDensities: no visible global function definition for 'lines'
plotDensities: no visible global function definition for 'legend'
plotErrorBarsLines: no visible global function definition for 'par'
plotErrorBarsLines: no visible global function definition for 'axis'
plotRIICor : <anonymous>: no visible global function definition for
'cor'
plotRIICor: no visible global function definition for 'data'
plotRIICor: no visible global function definition for 'boxplot'
plotRIICor: no visible global function definition for 'abline'
plotRTCor: no visible global function definition for 'cor'
plotRTCor: no visible global function definition for 'predict'
plotRTCor: no visible global function definition for 'lines'
plotRTCor: no visible global function definition for 'lowess'
plotRTCor: no visible global function definition for 'text'
plotRTResd: no visible global function definition for 'predict'
plotRTResd: no visible global function definition for 'abline'
plotRTResd: no visible global function definition for 'axis'
plotRTResd: no visible global function definition for 'text'
plotRelativeDensities: no visible global function definition for
'rainbow'
plotRelativeDensities: no visible global function definition for
'density'
plotRelativeDensities: no visible global function definition for
'na.omit'
plotRelativeDensities: no visible global function definition for
'abline'
plotRelativeDensities: no visible global function definition for
'lines'
plotStats: no visible global function definition for 'png'
plotStats: no visible global function definition for 'layout'
plotStats: no visible global function definition for 'barplot'
plotStats: no visible global function definition for 'dev.off'
plotStats: no visible global function definition for 'density'
plotStats: no visible global function definition for 'abline'
plotStats: no visible global function definition for 'aggregate'
plotStats: no visible global function definition for 'hist'
plotStats: no visible global function definition for 'par'
predictRT: no visible global function definition for 'cor'
predictRT: no visible global function definition for 'lm'
predictRT: no visible global function definition for 'predict'
quantification.accuracy: no visible global function definition for
'cor'
quantification.accuracy: no visible global function definition for
'median'
readLibFile: no visible global function definition for 'read.delim2'
reliabilityCheckLibrary: no visible global function definition for
'read.delim'
reliabilityCheckLibrary: no visible global function definition for
'png'
reliabilityCheckLibrary: no visible global function definition for
'barplot'
reliabilityCheckLibrary: no visible global function definition for
'gray'
reliabilityCheckLibrary: no visible global function definition for
'axis'
reliabilityCheckLibrary: no visible global function definition for
'points'
reliabilityCheckLibrary: no visible global function definition for
'mtext'
reliabilityCheckLibrary: no visible global function definition for
'par'
reliabilityCheckLibrary: no visible global function definition for
'legend'
reliabilityCheckLibrary: no visible global function definition for
'dev.off'
reliabilityCheckLibrary: no visible global function definition for
'write.csv'
reliabilityCheckSwath: no visible global function definition for
'flog.threshold'
reliabilityCheckSwath: no visible binding for global variable 'ERROR'
reliabilityCheckSwath: no visible global function definition for 'png'
reliabilityCheckSwath: no visible global function definition for
'layout'
reliabilityCheckSwath: no visible global function definition for
'density'
reliabilityCheckSwath: no visible global function definition for
'dev.off'
reliabilityCheckSwath: no visible global function definition for
'gray.colors'
reliabilityCheckSwath: no visible global function definition for 'par'
reliabilityCheckSwath: no visible global function definition for
'barplot'
reliabilityCheckSwath: no visible global function definition for
'legend'
reliabilityCheckSwath: no visible global function definition for
'terrain.colors'
reliabilityCheckSwath : <anonymous>: no visible global function
definition for 'aggregate'
reliabilityCheckSwath: no visible binding for global variable 'median'
reliabilityCheckSwath: no visible global function definition for
'boxplot'
reliabilityCheckSwath: no visible global function definition for
'write.csv'
selectModel: no visible global function definition for 'as.formula'
selectModel: no visible global function definition for 'predict'
selectModel: no visible global function definition for 'lm'
swath.means: no visible global function definition for 'aggregate'
swath.means : <anonymous>: no visible global function definition for
'na.omit'
Undefined global functions or variables:
ERROR abline aggregate as.formula axis barplot boxplot cor data
density dev.off flog.threshold gray gray.colors hist layout legend
lines lm lowess median mtext na.omit par png points predict rainbow
read.delim read.delim2 resid residuals sd segments t.test
terrain.colors text write.csv write.table
Consider adding
importFrom("grDevices", "dev.off", "gray", "gray.colors", "png",
"rainbow", "terrain.colors")
importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
"layout", "legend", "lines", "mtext", "par", "points",
"segments", "text")
importFrom("stats", "aggregate", "as.formula", "cor", "density", "lm",
"lowess", "median", "na.omit", "predict", "resid",
"residuals", "sd", "t.test")
importFrom("utils", "data", "read.delim", "read.delim2", "write.csv",
"write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: applyttest.Rd:27-28: Dropping empty section \details
prepare_Rd: applyttest.Rd:36-37: Dropping empty section \note
prepare_Rd: applyttest.Rd:34-35: Dropping empty section \author
prepare_Rd: applyttest.Rd:32-33: Dropping empty section \references
prepare_Rd: applyttestPep.Rd:26-27: Dropping empty section \details
prepare_Rd: applyttestPep.Rd:35-36: Dropping empty section \note
prepare_Rd: applyttestPep.Rd:33-34: Dropping empty section \author
prepare_Rd: applyttestPep.Rd:31-32: Dropping empty section \references
prepare_Rd: coverage.Rd:7-9: Dropping empty section \description
prepare_Rd: coverage.Rd:35-37: Dropping empty section \note
prepare_Rd: coverage.Rd:32-34: Dropping empty section \author
prepare_Rd: coverage.Rd:29-31: Dropping empty section \references
prepare_Rd: coverage.Rd:41-43: Dropping empty section \seealso
prepare_Rd: cv.Rd:7-9: Dropping empty section \description
prepare_Rd: cv.Rd:19-21: Dropping empty section \details
prepare_Rd: cv.Rd:31-33: Dropping empty section \note
prepare_Rd: cv.Rd:28-30: Dropping empty section \author
prepare_Rd: cv.Rd:25-27: Dropping empty section \references
prepare_Rd: cv.Rd:37-39: Dropping empty section \seealso
prepare_Rd: fdr.crit.Rd:7-9: Dropping empty section \description
prepare_Rd: fdr.crit.Rd:19-21: Dropping empty section \details
prepare_Rd: fdr.crit.Rd:22-28: Dropping empty section \value
prepare_Rd: fdr.crit.Rd:35-37: Dropping empty section \note
prepare_Rd: fdr.crit.Rd:32-34: Dropping empty section \author
prepare_Rd: fdr.crit.Rd:29-31: Dropping empty section \references
prepare_Rd: fdr.crit.Rd:41-43: Dropping empty section \seealso
prepare_Rd: getFdrBins.Rd:7-9: Dropping empty section \description
prepare_Rd: getFdrBins.Rd:22-24: Dropping empty section \details
prepare_Rd: getFdrBins.Rd:34-36: Dropping empty section \note
prepare_Rd: getFdrBins.Rd:31-33: Dropping empty section \author
prepare_Rd: getFdrBins.Rd:28-30: Dropping empty section \references
prepare_Rd: getFdrBins.Rd:40-42: Dropping empty section \seealso
prepare_Rd: medianNorm.Rd:17-18: Dropping empty section \details
prepare_Rd: medianNorm.Rd:26-27: Dropping empty section \note
prepare_Rd: medianNorm.Rd:24-25: Dropping empty section \author
prepare_Rd: medianNorm.Rd:22-23: Dropping empty section \references
prepare_Rd: medianNorm.Rd:30-31: Dropping empty section \seealso
prepare_Rd: mlr.Rd:20-21: Dropping empty section \details
prepare_Rd: mlr.Rd:32-33: Dropping empty section \note
prepare_Rd: mlr.Rd:30-31: Dropping empty section \author
prepare_Rd: mlr.Rd:36-37: Dropping empty section \seealso
prepare_Rd: mlrGroup.Rd:20-22: Dropping empty section \details
prepare_Rd: mlrGroup.Rd:31-32: Dropping empty section \note
prepare_Rd: mlrGroup.Rd:29-30: Dropping empty section \author
prepare_Rd: mlrrep.Rd:17-18: Dropping empty section \details
prepare_Rd: mlrrep.Rd:29-30: Dropping empty section \note
prepare_Rd: mlrrep.Rd:27-28: Dropping empty section \author
prepare_Rd: mlrrep.Rd:25-26: Dropping empty section \references
prepare_Rd: plotDensities.Rd:23-24: Dropping empty section \details
prepare_Rd: plotDensities.Rd:32-33: Dropping empty section \note
prepare_Rd: plotDensities.Rd:30-31: Dropping empty section \author
prepare_Rd: plotDensities.Rd:28-29: Dropping empty section \references
prepare_Rd: plotDensities.Rd:37-38: Dropping empty section \seealso
prepare_Rd: plotErrorBarsLines.Rd:35-36: Dropping empty section \details
prepare_Rd: plotErrorBarsLines.Rd:44-45: Dropping empty section \note
prepare_Rd: plotErrorBarsLines.Rd:42-43: Dropping empty section \author
prepare_Rd: plotErrorBarsLines.Rd:40-41: Dropping empty section \references
prepare_Rd: plotRelativeDensities.Rd:26-27: Dropping empty section \details
prepare_Rd: plotRelativeDensities.Rd:35-36: Dropping empty section \note
prepare_Rd: plotRelativeDensities.Rd:33-34: Dropping empty section \author
prepare_Rd: plotRelativeDensities.Rd:31-32: Dropping empty section \references
prepare_Rd: plotRelativeDensities.Rd:38-40: Dropping empty section \seealso
prepare_Rd: quantification.accuracy.Rd:7-9: Dropping empty section \description
prepare_Rd: quantification.accuracy.Rd:36-38: Dropping empty section \details
prepare_Rd: quantification.accuracy.Rd:50-52: Dropping empty section \note
prepare_Rd: quantification.accuracy.Rd:47-49: Dropping empty section \author
prepare_Rd: quantification.accuracy.Rd:44-46: Dropping empty section \references
prepare_Rd: quantification.accuracy.Rd:56-58: Dropping empty section \seealso
prepare_Rd: reliabilityCheckLibrary.Rd:7-9: Dropping empty section \description
prepare_Rd: reliabilityCheckLibrary.Rd:22-24: Dropping empty section \details
prepare_Rd: reliabilityCheckLibrary.Rd:34-36: Dropping empty section \note
prepare_Rd: reliabilityCheckLibrary.Rd:31-33: Dropping empty section \author
prepare_Rd: reliabilityCheckLibrary.Rd:28-30: Dropping empty section \references
prepare_Rd: reliabilityCheckLibrary.Rd:40-42: Dropping empty section \seealso
prepare_Rd: reliabilityCheckSwath.Rd:7-9: Dropping empty section \description
prepare_Rd: reliabilityCheckSwath.Rd:32-34: Dropping empty section \details
prepare_Rd: reliabilityCheckSwath.Rd:46-48: Dropping empty section \note
prepare_Rd: reliabilityCheckSwath.Rd:43-45: Dropping empty section \author
prepare_Rd: reliabilityCheckSwath.Rd:40-42: Dropping empty section \references
prepare_Rd: reliabilityCheckSwath.Rd:52-54: Dropping empty section \seealso
prepare_Rd: swath.means.Rd:7-9: Dropping empty section \description
prepare_Rd: swath.means.Rd:22-24: Dropping empty section \details
prepare_Rd: swath.means.Rd:34-36: Dropping empty section \note
prepare_Rd: swath.means.Rd:31-33: Dropping empty section \author
prepare_Rd: swath.means.Rd:28-30: Dropping empty section \references
prepare_Rd: swath.means.Rd:40-42: Dropping empty section \seealso
* 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 ... NOTE
Rd files without \description:
'coverage.Rd' 'cv.Rd' 'fdr.crit.Rd' 'getFdrBins.Rd'
'quantification.accuracy.Rd' 'reliabilityCheckLibrary.Rd'
'reliabilityCheckSwath.Rd' 'swath.means.Rd'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
reliabilityCheckSwath 36.67 3.73 40.58
quantification.accuracy 8.03 0.91 8.93
* 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: 3 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/SwathXtend.Rcheck/00check.log'
for details.
SwathXtend.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SwathXtend ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'SwathXtend' ... ** using staged installation ** R ** data ** 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 (SwathXtend)
SwathXtend.Rcheck/SwathXtend-Ex.timings
| name | user | system | elapsed | |
| applyttest | 0.3 | 0.0 | 0.3 | |
| applyttestPep | 0.15 | 0.03 | 0.19 | |
| buildSpectraLibPair | 1.89 | 0.02 | 1.96 | |
| canonicalFormat | 0.03 | 0.00 | 0.04 | |
| checkQuality | 1.30 | 0.03 | 1.34 | |
| cleanLib | 0.01 | 0.00 | 0.02 | |
| coverage | 0.02 | 0.00 | 0.01 | |
| cv | 0 | 0 | 0 | |
| fdr.crit | 1.17 | 0.14 | 1.55 | |
| getFdrBins | 3.08 | 0.58 | 3.81 | |
| medianNorm | 0.03 | 0.00 | 0.03 | |
| mlr | 0 | 0 | 0 | |
| mlrGroup | 0.02 | 0.01 | 0.03 | |
| mlrrep | 0.01 | 0.00 | 0.02 | |
| outputLib | 0.10 | 0.00 | 0.09 | |
| plotAll | 1.86 | 0.19 | 2.28 | |
| plotDensities | 0.12 | 0.00 | 0.13 | |
| plotErrorBarsLines | 0 | 0 | 0 | |
| plotRIICor | 0.13 | 0.05 | 0.17 | |
| plotRTCor | 1.20 | 0.01 | 1.22 | |
| plotRTResd | 1.3 | 0.0 | 1.3 | |
| plotRelativeDensities | 0.03 | 0.00 | 0.03 | |
| quantification.accuracy | 8.03 | 0.91 | 8.93 | |
| readLibFile | 0.06 | 0.00 | 0.07 | |
| reliabilityCheckLibrary | 0.50 | 0.08 | 1.01 | |
| reliabilityCheckSwath | 36.67 | 3.73 | 40.58 | |
| swath.means | 0.92 | 0.21 | 1.12 | |