Greg Finak
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/flowMerge |
| git_branch: RELEASE_3_17 |
| git_last_commit: d2db403 |
| git_last_commit_date: 2023-04-25 09:48:58 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 723/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowMerge 2.48.0 (landing page) Greg Finak
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the flowMerge 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: flowMerge |
| Version: 2.48.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMerge_2.48.0.tar.gz |
| StartedAt: 2023-10-17 20:06:31 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 20:09:16 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 165.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowMerge.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMerge_2.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowMerge.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMerge’ version ‘2.48.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
Depends: includes the non-default packages:
'graph', 'feature', 'flowClust', 'Rgraphviz', 'foreach', 'snow'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘flowMerge’ 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 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
Packages in Depends field not imported from:
‘foreach’ ‘snow’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initPFlowMerge: no visible global function definition for
‘clusterEvalQ’
mergeClusters: no visible global function definition for ‘%dopar%’
mergeClusters: no visible global function definition for ‘foreach’
mergeClusters: no visible global function definition for ‘%do%’
pFlowClust : <anonymous>: no visible global function definition for
‘clusterMap’
pFlowClust: no visible global function definition for ‘clusterMap’
ptree: no visible global function definition for ‘subGraph’
ptree: no visible global function definition for ‘nodes’
ptree : <anonymous>: no visible global function definition for
‘nodeDataDefaults<-’
ptree : <anonymous>: no visible global function definition for
‘nodeData<-’
ptree : <anonymous>: no visible global function definition for
‘subGraph’
ptree : <anonymous>: no visible global function definition for
‘nodeRenderInfo<-’
Undefined global functions or variables:
%do% %dopar% clusterEvalQ clusterMap foreach nodeData<-
nodeDataDefaults<- nodeRenderInfo<- nodes subGraph
* checking Rd files ... WARNING
checkRd: (7) NENT.Rd:22: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) checkForRemoteErrors.Rd:22: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) fitPiecewiseLinreg.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowMerge-class.Rd:53: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowMerge-package.Rd:29: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowMerge-package.Rd:29: Invalid email address: <raphael.gottardo@ircm.qc.ca>
checkRd: (7) flowMerge-package.Rd:31: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowObj-class.Rd:50: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowObj-class.Rd:50: Invalid email address: <raphael.gottardo@ircm.qc.ca>
checkRd: (7) flowObj.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowObj.Rd:23: Invalid email address: <raphael.gottardo@ircm.qc.ca>
checkRd: (7) initPFlowMerge.Rd:19: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) merge.Rd:26: Invalid email address: <greg.finak@ircm.qc.cq>
checkRd: (7) mergeClusters.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) mergeClusters2.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) pFlowClust.Rd:39: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) pFlowMerge.Rd:36: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) updateU.Rd:21: Invalid email address: <greg.finak@ircm.qc.ca>
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowMerge.Rcheck/00check.log’
for details.
flowMerge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowMerge ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘flowMerge’ ... ** using staged installation ** R ** data ** 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 (flowMerge)
flowMerge.Rcheck/flowMerge-Ex.timings
| name | user | system | elapsed | |
| NENT | 0.000 | 0.000 | 0.004 | |
| fitPiecewiseLinreg | 0 | 0 | 0 | |
| flowClust.res | 0.000 | 0.001 | 0.001 | |
| flowMerge-package | 0.000 | 0.000 | 0.001 | |
| flowObj | 0.000 | 0.001 | 0.003 | |
| map | 0.006 | 0.001 | 0.012 | |
| merge-methods | 0 | 0 | 0 | |
| merge | 0 | 0 | 0 | |
| pFlowMerge | 0.018 | 0.005 | 0.035 | |
| plot-methods | 0 | 0 | 0 | |
| updateU | 0 | 0 | 0 | |