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This page was generated on 2021-10-15 15:06:26 -0400 (Fri, 15 Oct 2021).

CHECK results for TurboNorm on tokay2

To the developers/maintainers of the TurboNorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TurboNorm.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 1975/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TurboNorm 1.40.0  (landing page)
Maarten van Iterson
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TurboNorm
git_branch: RELEASE_3_13
git_last_commit: 707184a
git_last_commit_date: 2021-05-19 11:47:01 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: TurboNorm
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TurboNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TurboNorm_1.40.0.tar.gz
StartedAt: 2021-10-15 07:02:26 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 07:04:57 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 150.3 seconds
RetCode: 0
Status:   OK  
CheckDir: TurboNorm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TurboNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TurboNorm_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TurboNorm.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TurboNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TurboNorm' version '1.40.0'
* 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 'TurboNorm' 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 ... NOTE
Packages in Depends field not imported from:
  'convert' 'limma' 'marray'
  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
normalize.AffyBatch.pspline: no visible global function definition for
  'intensity<-'
pspline: no visible global function definition for 'as'
pspline: no visible global function definition for 'maRb<-'
pspline: no visible global function definition for 'maGb<-'
pspline: no visible global function definition for 'maA'
pspline: no visible global function definition for 'maM'
pspline: no visible global function definition for 'layout'
pspline: no visible global function definition for 'maM<-'
pspline: no visible global function definition for 'lines'
turbotrend: no visible global function definition for 'median'
Undefined global functions or variables:
  as intensity<- layout lines maA maGb<- maM maM<- maRb<- median
Consider adding
  importFrom("graphics", "layout", "lines")
  importFrom("methods", "as")
  importFrom("stats", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/TurboNorm/libs/i386/TurboNorm.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/TurboNorm/libs/x64/TurboNorm.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
normalize.pspline 24.34   1.05   25.39
panel.pspline     11.87   0.22   12.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
normalize.pspline 26.37   0.77   27.22
panel.pspline     14.56   0.14   14.75
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/TurboNorm.Rcheck/00check.log'
for details.



Installation output

TurboNorm.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TurboNorm_1.40.0.tar.gz && rm -rf TurboNorm.buildbin-libdir && mkdir TurboNorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TurboNorm.buildbin-libdir TurboNorm_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TurboNorm_1.40.0.zip && rm TurboNorm_1.40.0.tar.gz TurboNorm_1.40.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 67  242k   67  163k    0     0   721k      0 --:--:-- --:--:-- --:--:--  722k
100  242k  100  242k    0     0   918k      0 --:--:-- --:--:-- --:--:--  917k

install for i386

* installing *source* package 'TurboNorm' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rinit.c -o Rinit.o
Rinit.c:8:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cMethods[] = {
                                        ^
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c binners.c -o binners.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o TurboNorm.dll tmp.def Rinit.o binners.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/TurboNorm.buildbin-libdir/00LOCK-TurboNorm/00new/TurboNorm/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TurboNorm'
    finding HTML links ... done
    methylation                             html  
    normalize.pspline                       html  
    panel.pspline                           html  
    pspline                                 html  
    turbonorm-package                       html  
    turbotrend                              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 'TurboNorm' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rinit.c -o Rinit.o
Rinit.c:8:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cMethods[] = {
                                        ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c binners.c -o binners.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o TurboNorm.dll tmp.def Rinit.o binners.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/TurboNorm.buildbin-libdir/TurboNorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TurboNorm' as TurboNorm_1.40.0.zip
* DONE (TurboNorm)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TurboNorm' successfully unpacked and MD5 sums checked

Tests output


Example timings

TurboNorm.Rcheck/examples_i386/TurboNorm-Ex.timings

nameusersystemelapsed
methylation0.100.000.09
normalize.pspline24.34 1.0525.39
panel.pspline11.87 0.2212.12
pspline3.640.033.67
turbotrend1.100.021.11

TurboNorm.Rcheck/examples_x64/TurboNorm-Ex.timings

nameusersystemelapsed
methylation0.060.020.08
normalize.pspline26.37 0.7727.22
panel.pspline14.56 0.1414.75
pspline2.720.012.73
turbotrend1.010.021.03