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CHECK report for iCNV on malbec2

This page was generated on 2018-10-17 08:31:24 -0400 (Wed, 17 Oct 2018).

Package 713/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCNV 1.0.0
Zilu Zhou
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/iCNV
Branch: RELEASE_3_7
Last Commit: 702eb35
Last Changed Date: 2018-04-30 10:35:50 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: iCNV
Version: 1.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:iCNV.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings iCNV_1.0.0.tar.gz
StartedAt: 2018-10-16 01:13:30 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:16:22 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 172.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: iCNV.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:iCNV.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings iCNV_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/iCNV.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCNV/DESCRIPTION’ ... OK
* this is package ‘iCNV’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iCNV’ can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/biocbuild/bbs-3.7-bioc/meat/iCNV.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iCNV_detection 12.428   0.12   12.62
* 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
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/iCNV.Rcheck/00check.log’
for details.



Installation output

iCNV.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL iCNV
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘iCNV’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iCNV)

Tests output


Example timings

iCNV.Rcheck/iCNV-Ex.timings

nameusersystemelapsed
bambaf_from_vcf4.4520.0804.837
bed_generator0.3880.0000.388
get_array_input0.0920.0040.123
iCNV_detection12.428 0.12012.620
icnv_output_to_gb0.0160.0000.017
normObj0.0040.0000.032
output_list0.0160.0000.016
plotHMMscore0.0920.0000.089
plot_intensity0.0920.0040.098
plotindi0.0600.0040.065
qcObj0.0000.0000.001