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CHECK report for snapCGH on malbec1

This page was generated on 2021-04-22 12:29:25 -0400 (Thu, 22 Apr 2021).

To the developers/maintainers of the snapCGH package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1741/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.60.0  (landing page)
John Marioni
Snapshot Date: 2021-04-21 14:50:06 -0400 (Wed, 21 Apr 2021)
URL: https://git.bioconductor.org/packages/snapCGH
Branch: RELEASE_3_12
Last Commit: 03e3471
Last Changed Date: 2020-10-27 10:27:53 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: snapCGH
Version: 1.60.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:snapCGH.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings snapCGH_1.60.0.tar.gz
StartedAt: 2021-04-22 06:01:33 -0400 (Thu, 22 Apr 2021)
EndedAt: 2021-04-22 06:04:21 -0400 (Thu, 22 Apr 2021)
EllapsedTime: 167.9 seconds
RetCode: 0
Status:   OK  
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:snapCGH.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings snapCGH_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/snapCGH.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snapCGH/DESCRIPTION’ ... OK
* this is package ‘snapCGH’ version ‘1.60.0’
* 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 ‘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 is not available
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/snapCGH.Rcheck/00check.log’
for details.



Installation output

snapCGH.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL snapCGH
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘snapCGH’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c optimizer.c -o optimizer.o
optimizer.c: In function ‘fr_two’:
optimizer.c:26:30: warning: unused variable ‘temp3’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:26:23: warning: unused variable ‘temp2’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:26:10: warning: unused variable ‘denom’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c: In function ‘fr_three’:
optimizer.c:195:30: warning: unused variable ‘temp3’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:195:23: warning: unused variable ‘temp2’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:195:10: warning: unused variable ‘denom’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c:194:69: warning: unused variable ‘alphahat’ [-Wunused-variable]
   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]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:413:23: warning: unused variable ‘temp2’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:413:10: warning: unused variable ‘denom’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c:412:69: warning: unused variable ‘alphahat’ [-Wunused-variable]
   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]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:687:23: warning: unused variable ‘temp2’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:687:10: warning: unused variable ‘denom’ [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c:686:69: warning: unused variable ‘alphahat’ [-Wunused-variable]
   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                     ^~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o snapCGH.so optimizer.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-snapCGH/00new/snapCGH/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (snapCGH)

Tests output


Example timings

snapCGH.Rcheck/snapCGH-Ex.timings

nameusersystemelapsed
LargeDataObject000
convert.output0.0000.0000.002
dim0.0040.0000.004