Multiple platform build/check report for BioC 3.8 - CHECK report for BAGS on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BAGS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BAGS_2.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BAGS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘2.22.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Gibbs2       56.352  0.184  56.592
DataGeneSets 12.732  0.224  13.027
MCMCDataSet  12.040  0.168  12.225
* 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-3.8-bioc/meat/BAGS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BAGS
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘BAGS’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BAGS.c -o BAGS.o
In file included from BAGS.c:8:0:
FuncionesFast-Final.h: In function ‘BetaFunCSDiff2’:
FuncionesFast-Final.h:145:70: warning: unused variable ‘YMu1’ [-Wunused-variable]
     double media1,media,varianza1,varianza,resultado,varaux0,varaux1,YMu1;
                                                                      ^
FuncionesFast-Final.h: In function ‘AlfaFunCS’:
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;
                                                                                                         ^
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:166:92: 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;
                                                                                            ^
BAGS.c: In function ‘Gibbs5’:
BAGS.c:25:48: warning: unused variable ‘resI’ [-Wunused-variable]
     double escala1,escala2,escala3,escala,rate,resI;
                                                ^
BAGS.c:25:43: warning: unused variable ‘rate’ [-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:25:28: warning: unused variable ‘escala3’ [-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:25:12: warning: unused variable ‘escala1’ [-Wunused-variable]
     double escala1,escala2,escala3,escala,rate,resI;
            ^
BAGS.c:24:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
     double formaAux;
            ^
BAGS.c:18:80: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
     double ResRho1,ResRho2,ResRho3,ResRho4,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA4,ResSgmA;
                                                                                ^
BAGS.c:15:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
               ^
BAGS.c: In function ‘Gibbs4’:
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:335:63: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
     double ResRho1,ResRho2,ResRho3,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA;
                                                               ^
BAGS.c:332:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
               ^
BAGS.c: In function ‘Gibbs3’:
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:593:36: 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: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:592:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
     double formaAux;
            ^
BAGS.c:586:46: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
     double ResRho1,ResRho2,ResSgmA1,ResSgmA2,ResSgmA;
                                              ^
BAGS.c:583:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
               ^
BAGS.c: In function ‘Gibbs2’:
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
                                           ^
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:786:20: 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:785:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
     double formaAux;
            ^
BAGS.c:779:29: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
     double ResRho1,ResSgmA1,ResSgmA;
                             ^
BAGS.c:776:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
               ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o BAGS.so BAGS.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (BAGS)

CHECK report for BAGS on malbec1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
AnnotationMFGO	0.044	0.000	0.045
BAGS-package	0.000	0.000	0.001
DataGeneSets	12.732	0.224	13.027
Gibbs2	56.352	0.184	56.592
Gibbs3	0	0	0
Gibbs4	0	0	0
Gibbs5	0	0	0
MCMCDataSet	12.040	0.168	12.225
ReadGMT	0	0	0