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This page was generated on 2022-06-24 11:07:15 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 snapCGH on palomino4


To the developers/maintainers of the snapCGH package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snapCGH.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1852/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.67.0  (landing page)
John Marioni
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/snapCGH
git_branch: master
git_last_commit: 2426aa7
git_last_commit_date: 2022-04-26 10:57:56 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: snapCGH
Version: 1.67.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings snapCGH_1.67.0.tar.gz
StartedAt: 2022-06-24 05:58:09 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 06:00:52 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 162.4 seconds
RetCode: 0
Status:   OK  
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings snapCGH_1.67.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/snapCGH.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.67.0'
* 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 'snapCGH' 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
* 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
heatmapGenome: no visible binding for global variable 'floor.func'
readPositionalInfo: no visible binding for global variable 'RGList'
Undefined global functions or variables:
  RGList floor.func
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/snapCGH/libs/x64/snapCGH.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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/snapCGH.Rcheck/00check.log'
for details.



Installation output

snapCGH.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/snapCGH_1.67.0.tar.gz && rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.67.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.67.0.zip && rm snapCGH_1.67.0.tar.gz snapCGH_1.67.0.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  617k  100  617k    0     0  5635k      0 --:--:-- --:--:-- --:--:-- 5667k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'snapCGH' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
   26 |   double denom, temp, temp2, temp3;
      |                              ^~~~~
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
   26 |   double denom, temp, temp2, temp3;
      |                       ^~~~~
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
   26 |   double denom, temp, temp2, temp3;
      |          ^~~~~
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
  195 |   double denom, temp, temp2, temp3;
      |                              ^~~~~
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
  195 |   double denom, temp, temp2, temp3;
      |                       ^~~~~
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
  195 |   double denom, temp, temp2, temp3;
      |          ^~~~~
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
  194 |   double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
      |                                                                     ^~~~~~~~
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
  413 |   double denom, temp, temp2, temp3;
      |                              ^~~~~
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
  413 |   double denom, temp, temp2, temp3;
      |                       ^~~~~
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
  413 |   double denom, temp, temp2, temp3;
      |          ^~~~~
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
  412 |   double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
      |                                                                     ^~~~~~~~
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
  687 |   double denom, temp, temp2, temp3;
      |                              ^~~~~
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
  687 |   double denom, temp, temp2, temp3;
      |                       ^~~~~
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
  687 |   double denom, temp, temp2, temp3;
      |          ^~~~~
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
  686 |   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
      |                                                                     ^~~~~~~~
gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs/x64
** R
** 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
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.67.0.zip
* DONE (snapCGH)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'snapCGH' successfully unpacked and MD5 sums checked

Tests output


Example timings

snapCGH.Rcheck/snapCGH-Ex.timings

nameusersystemelapsed
LargeDataObject000
convert.output0.010.000.01
dim0.020.000.02