Chen Meng
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/mogsa |
| git_branch: RELEASE_3_19 |
| git_last_commit: f3d45d4 |
| git_last_commit_date: 2024-04-30 10:42:59 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:39 -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 1315/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mogsa 1.38.0 (landing page) Chen Meng
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the mogsa 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: mogsa |
| Version: 1.38.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mogsa_1.38.0.tar.gz |
| StartedAt: 2024-05-06 23:08:05 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 23:09:07 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 61.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mogsa.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mogsa_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/mogsa.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 ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.38.0’
* 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 ‘mogsa’ 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) GIS.Rd:57: Lost braces; missing escapes or markup?
57 | log2(var(GS_{-i})/var(GS))
| ^
checkRd: (-1) GIS.Rd:59: Lost braces; missing escapes or markup?
59 | where GS is the gene set score, and the GS_{-i} is a recalculate of
| ^
checkRd: (-1) GIS.Rd:65: Lost braces; missing escapes or markup?
65 | log2(F(GS_{-i})/F(GS))
| ^
checkRd: (-1) mgsa-class.Rd:22-24: Lost braces
22 | \item{combine}{\code{signature(x = "mgsa", y = "mgsa")}}{
| ^
checkRd: (-1) NCI60_4array_supdata.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:33-35: 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
* 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
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/mogsa.Rcheck/00check.log’
for details.
mogsa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mogsa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘mogsa’ ... ** 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 (mogsa)
mogsa.Rcheck/mogsa-Ex.timings
| name | user | system | elapsed | |
| GIS | 0.292 | 0.006 | 0.298 | |
| annotate.gs | 0.052 | 0.002 | 0.054 | |
| bootMbpca | 0 | 0 | 0 | |
| bootMoa | 0 | 0 | 0 | |
| box.gs.feature | 0.066 | 0.003 | 0.070 | |
| combine-methods | 0.281 | 0.004 | 0.286 | |
| decompose.gs.group | 0.051 | 0.003 | 0.054 | |
| decompose.gs.ind | 0.046 | 0.002 | 0.048 | |
| distMoa | 0.103 | 0.004 | 0.108 | |
| getmgsa | 0.044 | 0.004 | 0.049 | |
| matpower | 0.001 | 0.000 | 0.000 | |
| mbpca | 0.880 | 0.022 | 0.902 | |
| mgsa-class | 0.082 | 0.002 | 0.084 | |
| moGap | 0.721 | 0.016 | 0.738 | |
| moa-class | 0.038 | 0.003 | 0.040 | |
| moa | 0.335 | 0.018 | 0.351 | |
| moa.sup-class | 0.046 | 0.006 | 0.052 | |
| moaCoef | 0.108 | 0.006 | 0.114 | |
| moaScore | 0.108 | 0.006 | 0.115 | |
| mogsa-package | 0.090 | 0.008 | 0.099 | |
| mogsa | 0.126 | 0.002 | 0.128 | |
| pairwise.rv | 0.005 | 0.000 | 0.006 | |
| plotGS | 0.052 | 0.002 | 0.054 | |
| prepGraphite | 0.106 | 0.002 | 0.108 | |
| prepMsigDB | 0.001 | 0.000 | 0.001 | |
| prepSupMoa | 1.897 | 0.047 | 1.948 | |
| softK | 0 | 0 | 0 | |
| sup.moa | 0.104 | 0.007 | 0.110 | |
| wsvd | 0.000 | 0.000 | 0.001 | |