Dorothee Childs
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/TPP |
| git_branch: RELEASE_3_19 |
| git_last_commit: 7c624fa |
| git_last_commit_date: 2024-04-30 10:43:07 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:48 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 2183/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TPP 3.32.0 (landing page) Dorothee Childs
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the TPP package: - 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: TPP |
| Version: 3.32.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP_3.32.0.tar.gz |
| StartedAt: 2024-05-07 01:32:47 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:35:14 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 146.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TPP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP_3.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/TPP.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TPP’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.8Mb
sub-directories of 1Mb or more:
data 1.9Mb
example_data 8.0Mb
test_data 1.9Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
Updated package vignette.
Cannot process chunk/lines:
Removed unit test that causes R CMD check to crash since the latest update of package 'testthat'.
Cannot process chunk/lines:
Fixed bug in plotColors for the case when no comparisons are specified
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘broom’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘doParallel:::.options’ ‘mefa:::rep.data.frame’
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
File ‘TPP/R/TPP.R’:
.onLoad calls:
packageStartupMessage(msgText, "\n")
See section ‘Good practice’ in '?.onAttach'.
fitSigmoidCCR: no visible global function definition for
‘capture.output’
modelSelector: no visible binding for global variable ‘testHypothesis’
modelSelector: no visible binding for global variable ‘fitMetric’
modelSelector: no visible binding for global variable ‘minMetric’
plot_fSta_distribution: no visible binding for global variable
‘density’
plot_pVal_distribution: no visible binding for global variable
‘..density..’
tpp2dCreateTPPTRreference: no visible binding for global variable
‘meltcurve_plot’
tpp2dCreateTPPTRreference: no visible binding for global variable
‘Protein_ID’
tpp2dExport: no visible binding for global variable ‘temperature’
tpp2dImport: no visible binding for global variable ‘temperature’
tpp2dNormalize: no visible binding for global variable ‘temperature’
Undefined global functions or variables:
..density.. capture.output density fitMetric meltcurve_plot minMetric
Protein_ID temperature testHypothesis
Consider adding
importFrom("stats", "density")
importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) analyzeTPPTR.Rd:146-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) analyzeTPPTR.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) analyzeTPPTR.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacCCR_data.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacCCR_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrCurveFit.Rd:42: Lost braces
42 | code{featureData(S)}.
| ^
checkRd: (-1) tppccrImport.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrImport.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrPlotCurves.Rd:45: Lost braces
45 | produced plots are stored in code{featureData(S)$plot}.
| ^
checkRd: (-1) tpptrImport.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tpptrImport.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tpptrImport.Rd:79: Lost braces in \itemize; meant \describe ?
* 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 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
analyzeTPPTR 8.061 0.048 8.139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/TPP.Rcheck/00check.log’
for details.
TPP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TPP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘TPP’ ... ** 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 (TPP)
TPP.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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.
> library(testthat)
> library(TPP)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
The following object is masked from 'package:testthat':
matches
>
> test_check("TPP")
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ]
>
> proc.time()
user system elapsed
68.139 1.597 74.039
TPP.Rcheck/TPP-Ex.timings
| name | user | system | elapsed | |
| analyze2DTPP | 1.562 | 0.024 | 1.588 | |
| analyzeTPPCCR | 0.999 | 0.013 | 1.016 | |
| analyzeTPPTR | 8.061 | 0.048 | 8.139 | |
| tpp2dAddAdditionalInfo | 0.006 | 0.000 | 0.007 | |
| tpp2dCalcFractAbundance | 0.696 | 0.037 | 0.733 | |
| tpp2dComputeFoldChanges | 0.109 | 0.002 | 0.110 | |
| tpp2dCreateDRplots | 2.846 | 0.022 | 2.873 | |
| tpp2dCurveFit | 1.536 | 0.020 | 1.569 | |
| tpp2dExport | 0.020 | 0.002 | 0.022 | |
| tpp2dImport | 0.093 | 0.002 | 0.095 | |
| tpp2dMerge2dRef | 1.864 | 0.020 | 1.887 | |
| tpp2dNormalize | 0.166 | 0.003 | 0.169 | |
| tpp2dSplineFitAndTest | 2.908 | 0.021 | 2.931 | |
| tpp2dSplinePlot | 0.003 | 0.000 | 0.004 | |
| tpp2dTRReferenceObject | 0.007 | 0.001 | 0.008 | |
| tppDefaultTheme | 0.129 | 0.001 | 0.131 | |
| tppExport | 0.130 | 0.010 | 0.145 | |
| tppQCPlotsCorrelateExperiments | 3.716 | 0.034 | 3.768 | |
| tppccrCurveFit | 1.023 | 0.008 | 1.032 | |
| tppccrImport | 0.031 | 0.001 | 0.032 | |
| tppccrNormalize | 0.037 | 0.001 | 0.038 | |
| tppccrNormalizeToReference | 0.051 | 0.002 | 0.053 | |
| tppccrPlotCurves | 1.488 | 0.020 | 1.512 | |
| tppccrResultTable | 0.937 | 0.010 | 0.948 | |
| tppccrTransform | 0.047 | 0.002 | 0.049 | |
| tpptrAnalyzeMeltingCurves | 0.099 | 0.001 | 0.101 | |
| tpptrCurveFit | 0.276 | 0.006 | 0.284 | |
| tpptrDefaultNormReqs | 0.103 | 0.002 | 0.105 | |
| tpptrFTest | 2.797 | 0.012 | 2.816 | |
| tpptrFitSplines | 0.318 | 0.006 | 0.325 | |
| tpptrImport | 0.055 | 0.002 | 0.057 | |
| tpptrNormalize | 0.102 | 0.002 | 0.104 | |
| tpptrPlotSplines | 2.776 | 0.014 | 2.797 | |
| tpptrSplineFitAndTest | 4.713 | 0.022 | 4.739 | |
| tpptrTidyUpESets | 0.105 | 0.004 | 0.110 | |