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CHECK report for SPEM on machv2

This page was generated on 2020-10-17 11:59:41 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SPEM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1709/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPEM 1.28.0
Xinyi YANG
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SPEM
Branch: RELEASE_3_11
Last Commit: 7b68b4a
Last Changed Date: 2020-04-27 14:33:47 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SPEM
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SPEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPEM_1.28.0.tar.gz
StartedAt: 2020-10-17 05:33:46 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:34:44 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 57.6 seconds
RetCode: 0
Status:  OK 
CheckDir: SPEM.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SPEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SPEM_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SPEM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPEM’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SPEM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘Rsolnp’ ‘methods’
  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
opt_parameter: no visible global function definition for ‘solnp’
SPEM,ExpressionSet: no visible global function definition for ‘exprs’
SPEM,ExpressionSet: no visible global function definition for ‘pData’
pre_prepare,ExpressionSet: no visible global function definition for
  ‘runif’
row_optimize,ExpressionSet: no visible global function definition for
  ‘exprs’
s_diff,ExpressionSet: no visible global function definition for ‘exprs’
s_diff,ExpressionSet: no visible global function definition for ‘pData’
s_diff,ExpressionSet : pre_smooth: no visible global function
  definition for ‘predict’
s_diff,ExpressionSet : pre_smooth: no visible global function
  definition for ‘smooth.spline’
Undefined global functions or variables:
  exprs pData predict runif smooth.spline solnp
Consider adding
  importFrom("stats", "predict", "runif", "smooth.spline")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
row_optimize 13.34  0.194  13.562
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SPEM.Rcheck/00check.log’
for details.



Installation output

SPEM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SPEM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SPEM’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (SPEM)

Tests output


Example timings

SPEM.Rcheck/SPEM-Ex.timings

nameusersystemelapsed
SPEM0.3900.0310.423
row_optimize13.340 0.19413.562
s_diff0.0910.0280.119
sos0.0020.0020.004