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This page was generated on 2022-01-17 13:06:25 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for iCNV on tokay2


To the developers/maintainers of the iCNV package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iCNV.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 908/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCNV 1.14.0  (landing page)
Zilu Zhou
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/iCNV
git_branch: RELEASE_3_14
git_last_commit: 8294aeb
git_last_commit_date: 2021-10-26 12:42:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: iCNV
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCNV.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iCNV_1.14.0.tar.gz
StartedAt: 2022-01-16 22:22:48 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 22:28:55 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 367.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: iCNV.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCNV.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iCNV_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iCNV.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iCNV/DESCRIPTION' ... OK
* this is package 'iCNV' version '1.14.0'
* 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 whether package 'iCNV' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.14-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
* 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
iCNV_detection  9.53   0.42   10.00
bambaf_from_vcf 4.23   0.80   16.47
get_array_input 0.08   0.06    9.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
iCNV_detection 9.02   0.14    9.44
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/iCNV.Rcheck/00check.log'
for details.



Installation output

iCNV.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iCNV_1.14.0.tar.gz && rm -rf iCNV.buildbin-libdir && mkdir iCNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iCNV.buildbin-libdir iCNV_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iCNV_1.14.0.zip && rm iCNV_1.14.0.tar.gz iCNV_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1215k  100 1215k    0     0  3873k      0 --:--:-- --:--:-- --:--:-- 3882k

install for i386

* installing *source* package 'iCNV' ...
** using staged installation
** 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
  converting help for package 'iCNV'
    finding HTML links ... done
    bambaf_from_vcf                         html  
    bed_generator                           html  
    chr                                     html  
    filenm                                  html  
    get_array_input                         html  
    iCNV_detection                          html  
    icnv_output_to_gb                       html  
    icnv_res0                               html  
    ngs_baf                                 html  
    ngs_baf.chr                             html  
    ngs_baf.id                              html  
    ngs_baf.nm                              html  
    ngs_baf.pos                             html  
    ngs_plr                                 html  
    ngs_plr.pos                             html  
    normObj                                 html  
    output_list                             html  
    plotHMMscore                            html  
    plot_intensity                          html  
    plotindi                                html  
    projname                                html  
    qcObj                                   html  
    sampname                                html  
    sampname_qc                             html  
    snp_baf                                 html  
    snp_baf.pos                             html  
    snp_lrr                                 html  
    snp_lrr.pos                             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 'iCNV' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCNV' as iCNV_1.14.0.zip
* DONE (iCNV)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'iCNV' successfully unpacked and MD5 sums checked

Tests output


Example timings

iCNV.Rcheck/examples_i386/iCNV-Ex.timings

nameusersystemelapsed
bambaf_from_vcf 4.23 0.8016.47
bed_generator0.420.000.42
get_array_input0.080.069.72
iCNV_detection 9.53 0.4210.00
icnv_output_to_gb0.010.000.02
normObj000
output_list0.020.000.01
plotHMMscore0.110.000.11
plot_intensity0.090.000.10
plotindi0.060.000.06
qcObj000

iCNV.Rcheck/examples_x64/iCNV-Ex.timings

nameusersystemelapsed
bambaf_from_vcf3.500.063.57
bed_generator0.30.00.3
get_array_input0.040.000.05
iCNV_detection9.020.149.44
icnv_output_to_gb0.010.000.01
normObj000
output_list0.020.000.02
plotHMMscore0.080.000.08
plot_intensity0.060.000.06
plotindi0.080.000.08
qcObj000