| Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:41 -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 1549/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phantasus 1.24.0 (landing page) Alexey Sergushichev
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the phantasus 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: phantasus |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phantasus_1.24.0.tar.gz |
| StartedAt: 2024-05-06 23:42:56 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 23:45:17 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 140.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: phantasus.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phantasus_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/phantasus.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 ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.24.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.env
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phantasus’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 29.0Mb
sub-directories of 1Mb or more:
testdata 5.0Mb
www 23.5Mb
* checking package 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 ... NOTE
Namespace in Imports field not imported from: 'rhdf5client'
All declared Imports should be used.
Unexported objects imported by ':::' calls:
'GEOquery:::.parseGPLTxt' 'GEOquery:::getDirListing'
'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac'
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
generatePreloadedSession: no visible binding for global variable 'es'
generatePreloadedSession: no visible binding for global variable
'heatmapJson'
getCountsMetaPart: no visible binding for global variable 'file_name'
getDesignMatrix: no visible binding for global variable 'id'
getFileIndexDF: no visible global function definition for '.'
getFileIndexDF: no visible binding for global variable 'Name'
getFileIndexDF: no visible binding for global variable 'Last modified'
getFileIndexDF: no visible binding for global variable 'Size'
limmaAnalysisSimpleImpl: no visible binding for global variable
'ComparisonTarget'
limmaAnalysisSimpleImpl: no visible binding for global variable
'ComparisonReference'
loadCounts: no visible global function definition for '.'
loadCounts: no visible binding for global variable 'directory'
loadCounts: no visible binding for global variable 'DT_counts_meta'
loadCounts: no visible binding for global variable 'accession'
loadCounts: no visible binding for global variable 'collection_type'
loadCounts: no visible binding for global variable 'file_name'
loadSession: no visible binding for global variable 'es'
servePhantasus: no visible global function definition for 'menu'
servePhantasus: no visible global function definition for
'install.packages'
setupPhantasus: no visible global function definition for 'menu'
setupPhantasus: no visible global function definition for
'install.packages'
validateCountsCollection: no visible binding for global variable
'file_name'
Undefined global functions or variables:
. accession collection_type ComparisonReference ComparisonTarget
directory DT_counts_meta es file_name heatmapJson id install.packages
Last modified menu Name Size
Consider adding
importFrom("utils", "install.packages", "menu")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:35-40: Dropping empty section \examples
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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/phantasus.Rcheck/00check.log’
for details.
phantasus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phantasus ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘phantasus’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (phantasus)
phantasus.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(phantasus)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/opencpu/config/defaults.conf
Loading config from /Users/biocbuild/Library/Preferences/org.R-project.R/R/opencpu/user.conf
>
> test_check("phantasus")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz'
Content type 'application/x-gzip' length 2848655 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1261/annot/GPL1261.annot.gz'
Content type 'application/x-gzip' length 8389179 bytes (8.0 MB)
==================================================
downloaded 8.0 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107746/matrix/GSE107746_series_matrix.txt.gz'
Content type 'application/x-gzip' length 7196 bytes
==================================================
downloaded 7196 bytes
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL20795&form=text&view=data'
downloaded 48 bytes
trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz'
trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz'
Content type 'application/x-gzip' length 596707 bytes (582 KB)
==================================================
downloaded 582 KB
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6103&form=text&view=data'
downloaded 3.4 MB
trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1273889 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6885&form=text&view=data'
downloaded 3.2 MB
trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1807552 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL1261&form=text&view=data'
downloaded 9.5 MB
trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz'
Content type 'application/x-gzip' length 1250109 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1807570 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz'
Content type 'application/x-gzip' length 1250109 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz'
Content type 'application/x-gzip' length 596708 bytes (582 KB)
==================================================
downloaded 582 KB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.annot.gz'
Content type 'application/x-gzip' length 4652589 bytes (4.4 MB)
==================================================
downloaded 4.4 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1273890 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6885/annot/GPL6885.annot.gz'
Content type 'application/x-gzip' length 4938348 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz'
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3386 bytes
==================================================
downloaded 3386 bytes
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
>
> proc.time()
user system elapsed
32.192 2.028 83.576
phantasus.Rcheck/phantasus-Ex.timings
| name | user | system | elapsed | |
| adjustDataset | 0 | 0 | 0 | |
| annotationDBMeta | 0 | 0 | 0 | |
| calcPCA | 0 | 0 | 0 | |
| checkGPLsFallback | 0.000 | 0.000 | 0.001 | |
| collapseDataset | 0 | 0 | 0 | |
| createES | 0 | 0 | 0 | |
| es | 0 | 0 | 0 | |
| generatePreloadedSession | 0 | 0 | 0 | |
| getCountsMetaPart | 0 | 0 | 0 | |
| getES | 0.000 | 0.001 | 0.000 | |
| getGDS | 0 | 0 | 0 | |
| getGSE | 0 | 0 | 0 | |
| limmaAnalysis | 0 | 0 | 0 | |
| loadGEO | 0 | 0 | 0 | |
| performKmeans | 0 | 0 | 0 | |
| queryAnnotationDBMeta | 0 | 0 | 0 | |
| read.gct | 0.021 | 0.001 | 0.021 | |
| reparseCachedESs | 0 | 0 | 0 | |
| reproduceInR | 0 | 0 | 0 | |
| servePhantasus | 0 | 0 | 0 | |
| write.gct | 0.018 | 0.000 | 0.020 | |