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CHECK report for BAGS on merida1

This page was generated on 2020-08-07 12:26:31 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BAGS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 104/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BAGS 2.29.0
Alejandro Quiroz-Zarate
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BAGS
Branch: master
Last Commit: 171d9d5
Last Changed Date: 2020-04-27 14:28:21 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BAGS
Version: 2.29.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BAGS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BAGS_2.29.0.tar.gz
StartedAt: 2020-08-06 23:39:18 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 23:41:39 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 141.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BAGS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BAGS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BAGS_2.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BAGS.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BAGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BAGS’ version ‘2.29.0’
* 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 ‘BAGS’ 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 ... NOTE
Package in Depends field not imported from: ‘Biobase’
  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 ... OK
* 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 is not available
* 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
Gibbs2       61.241 11.512  72.850
MCMCDataSet  15.262  0.871  16.150
DataGeneSets 13.095  0.748  13.863
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BAGS.Rcheck/00check.log’
for details.



Installation output

BAGS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BAGS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BAGS’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BAGS.c -o BAGS.o
In file included from BAGS.c:8:
./FuncionesFast-Final.h:145:70: warning: unused variable 'YMu1' [-Wunused-variable]
    double media1,media,varianza1,varianza,resultado,varaux0,varaux1,YMu1;
                                                                     ^
./FuncionesFast-Final.h:166:92: warning: unused variable 'C' [-Wunused-variable]
    double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
                                                                                           ^
./FuncionesFast-Final.h:166:94: warning: unused variable 'A' [-Wunused-variable]
    double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
                                                                                             ^
./FuncionesFast-Final.h:166:105: warning: unused variable 'MediaDiff' [-Wunused-variable]
    double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
                                                                                                        ^
BAGS.c:25:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                                          ^
BAGS.c:25:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                                               ^
BAGS.c:25:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                           ^
BAGS.c:25:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                                   ^
BAGS.c:25:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
           ^
BAGS.c:25:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                   ^
BAGS.c:24:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:342:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                               ^
BAGS.c:342:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                          ^
BAGS.c:342:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                   ^
BAGS.c:342:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                           ^
BAGS.c:342:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                   ^
BAGS.c:342:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
           ^
BAGS.c:341:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:593:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                               ^
BAGS.c:593:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                          ^
BAGS.c:593:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                   ^
BAGS.c:593:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
           ^
BAGS.c:593:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                   ^
BAGS.c:593:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                           ^
BAGS.c:592:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:785:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:786:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                   ^
BAGS.c:786:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
           ^
BAGS.c:786:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                   ^
BAGS.c:786:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                           ^
BAGS.c:786:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                               ^
BAGS.c:786:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                          ^
32 warnings generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BAGS.so BAGS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-BAGS/00new/BAGS/libs
** 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
** 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 (BAGS)

Tests output


Example timings

BAGS.Rcheck/BAGS-Ex.timings

nameusersystemelapsed
AnnotationMFGO0.0400.0080.047
BAGS-package000
DataGeneSets13.095 0.74813.863
Gibbs261.24111.51272.850
Gibbs30.0010.0010.001
Gibbs40.0000.0010.000
Gibbs50.0000.0010.001
MCMCDataSet15.262 0.87116.150
ReadGMT0.0000.0000.001