Liang-Bo Wang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/iGC |
| Branch: RELEASE_3_9 |
| Last Commit: b4c09bd |
| Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:33:57 -0400 (Wed, 16 Oct 2019).
| Package 798/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iGC 1.14.0 Liang-Bo Wang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: iGC |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iGC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iGC_1.14.0.tar.gz |
| StartedAt: 2019-10-16 04:31:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:32:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 52.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iGC.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iGC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iGC_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/iGC.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iGC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iGC' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : : no visible binding for global variable
'GENE'
direct_gene_cna : : 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 : : no
visible global function definition for 'na.omit'
find_cna_driven_gene : exp_grouptest_driven_by_cna : : 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/iGC.Rcheck/00check.log'
for details.
iGC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/iGC_1.14.0.tar.gz && rm -rf iGC.buildbin-libdir && mkdir iGC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iGC.buildbin-libdir iGC_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL iGC_1.14.0.zip && rm iGC_1.14.0.tar.gz iGC_1.14.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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100 2781k 100 2781k 0 0 14.1M 0 --:--:-- --:--:-- --:--:-- 14.6M
install for i386
* 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
converting help for package 'iGC'
finding HTML links ... done
create_gene_cna html
create_gene_exp html
create_sample_desc html
direct_gene_cna html
find_cna_driven_gene html
hg19DBNM html
iGC html
** 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
install for x64
* installing *source* package 'iGC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iGC' as iGC_1.14.0.zip
* DONE (iGC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'iGC' successfully unpacked and MD5 sums checked
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iGC.Rcheck/examples_i386/iGC-Ex.timings
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iGC.Rcheck/examples_x64/iGC-Ex.timings
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