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This page was generated on 2022-01-14 13:06:36 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 iterativeBMAsurv on tokay2


To the developers/maintainers of the iterativeBMAsurv package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iterativeBMAsurv.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 969/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.52.0  (landing page)
Ka Yee Yeung
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/iterativeBMAsurv
git_branch: RELEASE_3_14
git_last_commit: 9eebd34
git_last_commit_date: 2021-10-26 11:52:44 -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: iterativeBMAsurv
Version: 1.52.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.52.0.tar.gz
StartedAt: 2022-01-13 21:28:09 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 21:30:58 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 169.9 seconds
RetCode: 0
Status:   OK  
CheckDir: iterativeBMAsurv.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:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iterativeBMAsurv.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 'iterativeBMAsurv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iterativeBMAsurv' version '1.52.0'
* 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 whether package 'iterativeBMAsurv' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'survival'
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
  'BMA' 'leaps' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterateBMAsurv.train: no visible global function definition for
  'bic.surv'
iterateBMAsurv.train.wrapper: no visible global function definition for
  'bic.surv'
Undefined global functions or variables:
  bic.surv
* checking Rd files ... NOTE
prepare_Rd: predictBicSurv.Rd:46: Dropping empty section \note
prepare_Rd: predictiveAssessCategory.Rd:52: Dropping empty section \note
prepare_Rd: printTopGenes.Rd:49: Dropping empty section \note
prepare_Rd: singleGeneCoxph.Rd:54: Dropping empty section \note
prepare_Rd: testCens.Rd:13-14: Dropping empty section \details
prepare_Rd: testSurv.Rd:13-14: Dropping empty section \details
prepare_Rd: trainCens.Rd:13-14: Dropping empty section \details
prepare_Rd: trainSurv.Rd:13-14: Dropping empty section \details
* 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
imageplot.iterate.bma.surv 12.20   0.09   12.31
iterateBMAsurv.train        5.56   0.05    5.61
predictiveAssessCategory    5.35   0.03    5.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   14.24   0.03   14.31
iterateBMAsurv.train.wrapper  6.48   0.00    6.60
iterateBMAsurv.train          5.88   0.02    5.90
predictBicSurv                5.83   0.05    5.88
predictiveAssessCategory      5.78   0.01    5.80
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/iterativeBMAsurv.Rcheck/00check.log'
for details.



Installation output

iterativeBMAsurv.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iterativeBMAsurv_1.52.0.tar.gz && rm -rf iterativeBMAsurv.buildbin-libdir && mkdir iterativeBMAsurv.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iterativeBMAsurv_1.52.0.zip && rm iterativeBMAsurv_1.52.0.tar.gz iterativeBMAsurv_1.52.0.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 62862  100 62862    0     0   574k      0 --:--:-- --:--:-- --:--:--  579k

install for i386

* installing *source* package 'iterativeBMAsurv' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iterativeBMAsurv'
    finding HTML links ... done
    crossVal                                html  
    imageplot.iterate.bma.surv              html  
    iterateBMAsurv.train                    html  
    iterateBMAsurv.train.predict.assess     html  
    iterateBMAsurv.train.wrapper            html  
    iterativeBMAsurv-internal               html  
    iterativeBMAsurv-package                html  
    predictBicSurv                          html  
    predictiveAssessCategory                html  
    printTopGenes                           html  
    singleGeneCoxph                         html  
    testCens                                html  
    testData                                html  
    testSurv                                html  
    trainCens                               html  
    trainData                               html  
    trainSurv                               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 'iterativeBMAsurv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iterativeBMAsurv' as iterativeBMAsurv_1.52.0.zip
* DONE (iterativeBMAsurv)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'iterativeBMAsurv' successfully unpacked and MD5 sums checked

Tests output


Example timings

iterativeBMAsurv.Rcheck/examples_i386/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal1.860.031.89
imageplot.iterate.bma.surv12.20 0.0912.31
iterateBMAsurv.train5.560.055.61
iterateBMAsurv.train.predict.assess0.670.010.68
iterateBMAsurv.train.wrapper4.970.005.00
iterativeBMAsurv-package2.080.032.11
predictBicSurv4.940.044.97
predictiveAssessCategory5.350.035.39
printTopGenes0.360.000.36
singleGeneCoxph0.380.010.39

iterativeBMAsurv.Rcheck/examples_x64/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal2.250.033.07
imageplot.iterate.bma.surv14.24 0.0314.31
iterateBMAsurv.train5.880.025.90
iterateBMAsurv.train.predict.assess0.840.010.85
iterateBMAsurv.train.wrapper6.480.006.60
iterativeBMAsurv-package2.830.052.87
predictBicSurv5.830.055.88
predictiveAssessCategory5.780.015.80
printTopGenes0.350.020.35
singleGeneCoxph0.350.010.38