Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 979/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iGC 1.30.0 (landing page) Liang-Bo Wang
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the iGC 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: iGC |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iGC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iGC_1.30.0.tar.gz |
StartedAt: 2023-10-18 01:32:24 -0400 (Wed, 18 Oct 2023) |
EndedAt: 2023-10-18 01:33:17 -0400 (Wed, 18 Oct 2023) |
EllapsedTime: 52.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: iGC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iGC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iGC_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/iGC.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 ‘iGC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iGC’ version ‘1.30.0’ * 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 ‘iGC’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: extdata 5.6Mb * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE create_gene_cna: no visible global function definition for ‘data’ create_gene_cna: no visible binding for global variable ‘hg19DBNM’ create_gene_cna: no visible binding for global variable ‘Gene.Symbol’ create_gene_cna: no visible binding for global variable ‘GENE’ direct_gene_cna : <anonymous>: no visible binding for global variable ‘GENE’ direct_gene_cna : <anonymous>: no visible binding for global variable ‘gain_loss’ direct_gene_cna: no visible binding for global variable ‘GENE’ find_cna_driven_gene: no visible binding for global variable ‘GENE’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding for global variable ‘Gain’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding for global variable ‘GENE’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding for global variable ‘Loss’ find_cna_driven_gene : exp_grouptest_driven_by_cna : <anonymous>: no visible global function definition for ‘na.omit’ find_cna_driven_gene : exp_grouptest_driven_by_cna : <anonymous>: no visible global function definition for ‘t.test’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible global function definition for ‘p.adjust’ find_cna_driven_gene: no visible binding for global variable ‘p_value’ find_cna_driven_gene: no visible binding for global variable ‘fdr’ find_cna_driven_gene: no visible binding for global variable ‘vs_rest_exp_diff’ process_cna_per_sample: no visible binding for global variable ‘gain_loss’ process_cna_per_sample: no visible binding for global variable ‘Segment_Mean’ process_cna_per_sample: no visible binding for global variable ‘Chromosome’ process_cna_per_sample: no visible binding for global variable ‘Start’ process_cna_per_sample: no visible binding for global variable ‘End’ process_cna_per_sample: no visible binding for global variable ‘Gene.Symbol’ process_cna_per_sample: no visible binding for global variable ‘cur_sample’ process_cna_per_sample_direct: no visible binding for global variable ‘Segment_Mean’ process_cna_per_sample_direct: no visible binding for global variable ‘gain_loss’ process_cna_per_sample_direct: no visible binding for global variable ‘cna_val’ read_cna_geo: no visible binding for global variable ‘GENE’ read_cna_geo: no visible binding for global variable ‘Segment_Mean’ read_gene_exp: no visible global function definition for ‘read.table’ Undefined global functions or variables: Chromosome End GENE Gain Gene.Symbol Loss Segment_Mean Start cna_val cur_sample data fdr gain_loss hg19DBNM na.omit p.adjust p_value read.table t.test vs_rest_exp_diff Consider adding importFrom("stats", "na.omit", "p.adjust", "t.test") importFrom("utils", "data", "read.table") 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 LazyData ... 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/iGC.Rcheck/00check.log’ for details.
iGC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iGC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘iGC’ ... ** 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 (iGC)
iGC.Rcheck/iGC-Ex.timings
name | user | system | elapsed | |
create_gene_cna | 0.930 | 0.036 | 1.483 | |
create_gene_exp | 0.082 | 0.008 | 0.134 | |
create_sample_desc | 0.004 | 0.002 | 0.009 | |
direct_gene_cna | 0.024 | 0.002 | 0.039 | |
find_cna_driven_gene | 0.057 | 0.003 | 0.089 | |