Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:07:15 -0500 (Wed, 19 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 RIPAT on tokay2


To the developers/maintainers of the RIPAT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RIPAT.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 1612/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPAT 1.4.0  (landing page)
Min-Jeong Baek
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/RIPAT
git_branch: RELEASE_3_14
git_last_commit: 8b46270
git_last_commit_date: 2021-10-26 13:02:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RIPAT
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RIPAT_1.4.0.tar.gz
StartedAt: 2022-01-19 01:23:28 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 01:25:47 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 139.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RIPAT.Rcheck
Warnings: 0

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:RIPAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RIPAT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RIPAT.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 'RIPAT/DESCRIPTION' ... OK
* this is package 'RIPAT' version '1.4.0'
* 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 'RIPAT' 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
* 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
annoByCpG: no visible global function definition for 'hist'
annoByCpG: no visible binding for global variable 'Range'
annoByCpG: no visible binding for global variable 'Freq'
annoByCpG: no visible binding for global variable 'Group'
annoByGene: no visible global function definition for 'hist'
annoByGene: no visible binding for global variable 'Range'
annoByGene: no visible binding for global variable 'Freq'
annoByGene: no visible binding for global variable 'Group'
annoByRepeat: no visible global function definition for 'hist'
annoByRepeat: no visible binding for global variable 'all_dist_dup_m'
annoByRepeat: no visible binding for global variable 'Range'
annoByRepeat: no visible binding for global variable 'Freq'
annoByRepeat: no visible binding for global variable 'Group'
annoByVar: no visible global function definition for 'hist'
annoByVar: no visible binding for global variable 'Range'
annoByVar: no visible binding for global variable 'Freq'
annoByVar: no visible binding for global variable 'Group'
makeDocument : <anonymous>: no visible global function definition for
  'hist'
makeDocument: no visible binding for global variable 'group'
makeDocument: no visible binding for global variable 'type'
makeDocument: no visible binding for global variable 'convert_p'
makeDocument: no visible global function definition for 'par'
Undefined global functions or variables:
  Freq Group Range all_dist_dup_m convert_p group hist par type
Consider adding
  importFrom("graphics", "hist", "par")
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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
makeData     10.58   0.18   12.03
drawingKaryo  9.26   1.09   10.35
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
drawingKaryo 11.41   0.38   11.78
makeData      8.86   0.12   10.11
makeDocument  4.77   0.60    5.53
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RIPAT.Rcheck/00check.log'
for details.



Installation output

RIPAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RIPAT_1.4.0.tar.gz && rm -rf RIPAT.buildbin-libdir && mkdir RIPAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPAT.buildbin-libdir RIPAT_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RIPAT_1.4.0.zip && rm RIPAT_1.4.0.tar.gz RIPAT_1.4.0.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
  3 2810k    3   98k    0     0   752k      0  0:00:03 --:--:--  0:00:03  754k
100 2810k  100 2810k    0     0  4560k      0 --:--:-- --:--:-- --:--:-- 4561k

install for i386

* installing *source* package 'RIPAT' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RIPAT'
    finding HTML links ... done
    annoByCpG                               html  
    annoByGene                              html  
    annoByRepeat                            html  
    annoByVar                               html  
    blast_gene                              html  
    blast_obj                               html  
    cpg_exam_db                             html  
    drawingKaryo                            html  
    gene_exam_db                            html  
    makeData                                html  
    makeDocument                            html  
    makeInputObj                            html  
    makeInputObj2                           html  
    micro_exam_db                           html  
    repeat_exam_db                          html  
    tss_exam_db                             html  
    var_exam_db                             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 'RIPAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPAT' as RIPAT_1.4.0.zip
* DONE (RIPAT)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RIPAT' successfully unpacked and MD5 sums checked

Tests output


Example timings

RIPAT.Rcheck/examples_i386/RIPAT-Ex.timings

nameusersystemelapsed
annoByCpG3.890.314.20
annoByGene1.330.071.39
annoByRepeat1.200.061.27
annoByVar0.800.020.81
blast_gene0.080.000.08
blast_obj000
cpg_exam_db0.000.010.02
drawingKaryo 9.26 1.0910.35
gene_exam_db0.050.000.05
makeData10.58 0.1812.03
makeDocument3.421.154.69
makeInputObj1.000.321.94
makeInputObj20.740.000.74
micro_exam_db000
repeat_exam_db0.010.000.01
tss_exam_db0.050.000.05
var_exam_db0.090.000.09

RIPAT.Rcheck/examples_x64/RIPAT-Ex.timings

nameusersystemelapsed
annoByCpG4.410.144.55
annoByGene1.600.051.65
annoByRepeat1.550.061.61
annoByVar0.920.010.94
blast_gene0.10.00.1
blast_obj000
cpg_exam_db0.010.000.01
drawingKaryo11.41 0.3811.78
gene_exam_db0.030.000.03
makeData 8.86 0.1210.11
makeDocument4.770.605.53
makeInputObj0.900.030.94
makeInputObj20.670.000.67
micro_exam_db000
repeat_exam_db0.020.000.01
tss_exam_db0.030.000.04
var_exam_db0.080.000.07