Caitlin McHugh
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/cpvSNP |
| git_branch: RELEASE_3_17 |
| git_last_commit: f8f1461 |
| git_last_commit_date: 2023-04-25 10:36:47 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -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 446/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cpvSNP 1.32.0 (landing page) Caitlin McHugh
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the cpvSNP 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: cpvSNP |
| Version: 1.32.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cpvSNP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cpvSNP_1.32.0.tar.gz |
| StartedAt: 2023-10-17 12:32:40 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 12:41:26 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 526.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cpvSNP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cpvSNP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cpvSNP_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cpvSNP.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 ‘cpvSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cpvSNP’ version ‘1.32.0’
* 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 ‘cpvSNP’ 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
'library' or 'require' call to ‘GSEABase’ which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assocPvalBySetPlot: no visible global function definition for ‘rgb’
assocPvalBySetPlot: no visible global function definition for ‘col2rgb’
assocPvalBySetPlot : <anonymous>: no visible global function definition
for ‘density’
assocPvalBySetPlot: no visible global function definition for ‘legend’
assocPvalBySetPlot: no visible global function definition for ‘polygon’
assocPvalBySetPlot: no visible global function definition for ‘lines’
assocPvalBySetPlot: no visible global function definition for ‘points’
createArrayData: no visible global function definition for ‘GRanges’
createArrayData: no visible global function definition for ‘Rle’
createArrayData: no visible global function definition for ‘IRanges’
createArrayData: no visible global function definition for
‘elementMetadata<-’
geneToSNPList: no visible global function definition for ‘findOverlaps’
glossiMarginal: no visible global function definition for ‘pgamma’
plotPvals: no visible binding for global variable ‘df’
plotPvals: no visible binding for global variable ‘pval’
simulate_chisq: no visible global function definition for ‘rnorm’
vegasMarginal: no visible global function definition for ‘rbinom’
vegasMarginal: no visible global function definition for ‘qchisq’
vegasPrep: no visible global function definition for ‘elementMetadata’
show,VEGASResult: no visible global function definition for ‘var’
Undefined global functions or variables:
GRanges IRanges Rle col2rgb density df elementMetadata
elementMetadata<- findOverlaps legend lines pgamma points polygon
pval qchisq rbinom rgb rnorm var
Consider adding
importFrom("grDevices", "col2rgb", "rgb")
importFrom("graphics", "legend", "lines", "points", "polygon")
importFrom("stats", "density", "df", "pgamma", "qchisq", "rbinom",
"rnorm", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* 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
geneToSNPList 5.839 0.361 10.745
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cpvSNP.Rcheck/00check.log’
for details.
cpvSNP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cpvSNP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘cpvSNP’ ... ** 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 (cpvSNP)
cpvSNP.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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.
> BiocGenerics:::testPackage("cpvSNP")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
making GRanges object
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
Warning: coercing ldMatrix from data.frame to matrix.
RUNIT TEST PROTOCOL -- Tue Oct 17 12:41:11 2023
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
cpvSNP RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
Warning message:
In mode(current) : NAs introduced by coercion
>
> proc.time()
user system elapsed
20.070 1.048 30.470
cpvSNP.Rcheck/cpvSNP-Ex.timings
| name | user | system | elapsed | |
| GLOSSIResult-class | 0.002 | 0.001 | 0.004 | |
| GLOSSIResultCollection-class | 0.001 | 0.000 | 0.001 | |
| GeneSetResult-class | 0.001 | 0.001 | 0.005 | |
| GeneSetResultCollection-class | 0.001 | 0.001 | 0.000 | |
| VEGASResult-class | 0.000 | 0.001 | 0.003 | |
| VEGASResultCollection-class | 0.001 | 0.001 | 0.001 | |
| createArrayData | 0.224 | 0.016 | 0.433 | |
| degreesOfFreedom-method | 0 | 0 | 0 | |
| geneSetAnalysis | 0.158 | 0.010 | 0.315 | |
| geneSetName-methods | 0.000 | 0.000 | 0.001 | |
| geneToSNPList | 5.839 | 0.361 | 10.745 | |
| glossi | 0.006 | 0.004 | 0.020 | |
| glossiMarginal | 0.002 | 0.001 | 0.005 | |
| pValue-method | 0 | 0 | 0 | |
| simulatedStats-method | 0 | 0 | 0 | |
| statistic-methods | 0 | 0 | 0 | |