| Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:06 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 127/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BaseSpaceR 1.46.0 (landing page) Jared O'Connell
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the BaseSpaceR 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: BaseSpaceR |
| Version: 1.46.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BaseSpaceR_1.46.0.tar.gz |
| StartedAt: 2024-04-17 06:21:14 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 06:22:26 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 71.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BaseSpaceR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BaseSpaceR_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BaseSpaceR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.46.0’
* 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 ‘BaseSpaceR’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
BUG FIXES
Cannot process chunk/lines:
Changed Access token and projects ID used in the vignette to reflect changes in
Cannot process chunk/lines:
the permission enforcements performed by BaseSpace
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Rsamtools’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for ‘BamFile’
GET,ServiceURI: no visible global function definition for
‘basicHeaderGatherer’
GET,ServiceURI: no visible global function definition for
‘basicTextGatherer’
GET,ServiceURI: no visible global function definition for ‘getForm’
GET,ServiceURI: no visible global function definition for ‘curlOptions’
POST,ServiceURI: no visible global function definition for
‘basicHeaderGatherer’
POST,ServiceURI: no visible global function definition for
‘basicTextGatherer’
POST,ServiceURI: no visible global function definition for
‘curlPerform’
POSTForm,ServiceURI: no visible global function definition for
‘basicHeaderGatherer’
POSTForm,ServiceURI: no visible global function definition for
‘basicTextGatherer’
POSTForm,ServiceURI: no visible global function definition for
‘postForm’
POSTForm,ServiceURI: no visible global function definition for
‘curlOptions’
getBAMs,AppResults: no visible binding for global variable
‘BamFileList’
getFiles,AppAuth : .toDisk: no visible global function definition for
‘CFILE’
getFiles,AppAuth : .toDisk: no visible global function definition for
‘curlPerform’
getFiles,AppAuth : .toMem: no visible global function definition for
‘getURLContent’
getFiles,AppAuth : .toMem: no visible binding for global variable
‘dsize’
Undefined global functions or variables:
BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
curlOptions curlPerform dsize getForm getURLContent postForm
* checking Rd files ... WARNING
checkRd: (5) Genomes-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) Genomes-class.Rd:53-58: \item in \describe must have non-empty label
checkRd: (5) Genomes-class.Rd:59-62: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:55-58: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:55-58: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:63-66: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:67-72: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:73-76: \item in \describe must have non-empty label
checkRd: (5) Users-class.Rd:33-36: \item in \describe must have non-empty label
checkRd: (5) Users-class.Rd:37-41: \item in \describe must have non-empty label
* 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
Runs-class 0.162 0.011 6.560
Projects-class 0.120 0.008 5.716
Samples-class 0.112 0.007 6.553
* 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-3.18-bioc-mac-arm64/meat/BaseSpaceR.Rcheck/00check.log’
for details.
BaseSpaceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BaseSpaceR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘BaseSpaceR’ ... ** 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 (BaseSpaceR)
BaseSpaceR.Rcheck/BaseSpaceR-Ex.timings
| name | user | system | elapsed | |
| AppAuth-class | 0.124 | 0.019 | 1.255 | |
| AppResults-class | 0.001 | 0.000 | 0.001 | |
| AppSessionAuth | 0.001 | 0.000 | 0.001 | |
| AppSessions-class | 0.001 | 0.001 | 0.000 | |
| Coverage | 0.012 | 0.002 | 0.014 | |
| Error | 0.001 | 0.000 | 0.000 | |
| Files-class | 0.072 | 0.009 | 3.390 | |
| FilesExtra | 0.081 | 0.007 | 2.885 | |
| Genomes-class | 0.106 | 0.009 | 1.760 | |
| Projects-class | 0.120 | 0.008 | 5.716 | |
| Response-class | 0.002 | 0.001 | 0.002 | |
| Runs-class | 0.162 | 0.011 | 6.560 | |
| Samples-class | 0.112 | 0.007 | 6.553 | |
| ServiceURI-class | 0.001 | 0.000 | 0.001 | |
| Users-class | 0.065 | 0.007 | 2.110 | |
| Variants | 0.064 | 0.006 | 1.991 | |
| data-aAuth | 0.033 | 0.004 | 0.446 | |