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BioC 3.2: CHECK report for XDE on oaxaca

This page was generated on 2016-04-23 10:23:54 -0700 (Sat, 23 Apr 2016).

Package 1098/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XDE 2.16.0
Robert Scharpf
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/XDE
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: XDE
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XDE_2.16.0.tar.gz
StartedAt: 2016-04-23 05:20:33 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:23:20 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 167.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: XDE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XDE_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/XDE.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘2.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  data/.commands.R
  data/.createLogFiles.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘XDE’ can be installed ... [33s/33s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘graphics’ ‘methods’ ‘genefilter’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘GeneMeta’ ‘RColorBrewer’ ‘genefilter’ ‘siggenes’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘graphics:::pairs’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘pairs’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
$,XdeMcmc: warning in matrix(mcmc, nr = iterations(x), nc =
  length(studyNames(x)), byrow = byrow): partial argument match of 'nr'
  to 'nrow'
$,XdeMcmc: warning in matrix(mcmc, nr = iterations(x), nc =
  length(studyNames(x)), byrow = byrow): partial argument match of 'nc'
  to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = 1, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = S * (S - 1)/2, byrow = TRUE):
  partial argument match of 'nc' to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = 18, nr = iterations(x), byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
$,XdeMcmc: warning in matrix(mcmc, nc = 18, nr = iterations(x), byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
.studySplit,ExpressionSet : .local: warning in matrix(1, nr =
  nrow(eset[[1]]), nc = nsplit): partial argument match of 'nr' to
  'nrow'
.studySplit,ExpressionSet : .local: warning in matrix(1, nr =
  nrow(eset[[1]]), nc = nsplit): partial argument match of 'nc' to
  'ncol'
computeGOF: no visible binding for global variable ‘psi’
modelA_B_MIupdates: no visible binding for global variable ‘x’
modelA_B_MIupdates: no visible binding for global variable ‘d’
rupdateBDDeltaStar_HyperInverseWishart: no visible binding for global
  variable ‘phenodata’
ssStatistic : sam.wrapper: no visible global function definition for
  ‘sam’
ssStatistic : z.wrapper: no visible global function definition for
  ‘zScores’
pairs,matrix : panel: no visible global function definition for
  ‘brewer.pal’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'ExpressionSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [5s/5s]
 [5s/6s] 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/XDE.Rcheck/00check.log’
for details.


XDE.Rcheck/00install.out:

* installing *source* package ‘XDE’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Cholesky.cpp -o Cholesky.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Matrix_v2.cpp -o Matrix_v2.o
In file included from Matrix_v2.cpp:1:
./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable]
  int k = 1;
      ^
Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j,r;
        ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison]
        if (theGene[k][i] == 1) include == 1;
                                ˜˜˜˜˜˜˜˜^˜˜˜
Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment
        if (theGene[k][i] == 1) include == 1;
                                        ^˜
                                        =
Potential_v2.cpp:876:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  if (omega0 = 0.0)
      ˜˜˜˜˜˜˜^˜˜˜˜
Potential_v2.cpp:876:14: note: place parentheses around the assignment to silence this warning
  if (omega0 = 0.0)
             ^
      (           )
Potential_v2.cpp:876:14: note: use '==' to turn this assignment into an equality comparison
  if (omega0 = 0.0)
             ^
             ==
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable]
  double x,y,tt,sum;
         ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Rinterface_v2.cpp:2:
In file included from ./Update_v2.h:8:
./Random.h:19:9: warning: 'PI' macro redefined
#define PI         3.14159265
        ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:9: note: previous definition is here
#define PI             M_PI
        ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Structure.cpp -o Structure.o
Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable]
  char c;
       ^
Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable]
          int nRead = sscanf(var1,"%d",&value);
              ^
Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable]
              int nRead = sscanf(var2,"%le",&value);
                  ^
Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable]
      char c;
           ^
Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable]
      char c;
           ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable]
  double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta,
         ^
Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable]
  double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues,
         ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable]
    double detPrior = inverse(var,varInv);
           ^
Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable]
    double detPosterior = 1.0 /inverse(varInv,var);
           ^
Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable]
    int s;
        ^
Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable]
    double detPrior = inverse(var,varInv);
           ^
Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable]
    double detPosterior = 1.0 / inverse(varInv,var);
           ^
Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable]
        int ngg = neighbour[gg].size();
            ^
Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable]
          int ngg = neighbour[gg].size();
              ^
Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable]
      map<int,double>::iterator itextra = VinvSparse[k].end();
                                ^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
./Random.h:19:9: warning: 'PI' macro redefined
#define PI         3.14159265
        ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:9: note: previous definition is here
#define PI             M_PI
        ^
1 warning generated.
clang++ -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 XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/XDE.Rcheck/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘pairs’ from package ‘graphics’ in package ‘XDE’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘XDE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (XDE)

XDE.Rcheck/XDE-Ex.timings:

nameusersystemelapsed
ExpressionSetList-class0.0340.0060.039
Parameters-class0.0020.0000.003
XdeMcmc-class0.0010.0000.001
XdeParameter-class0.0030.0010.003
burnin0.0010.0000.000
empiricalStart0.1960.0080.204
expressionSetList0.0150.0030.019
firstMcmc0.1540.0040.159
geneCenter0.0770.0040.080
hyperparameters0.1910.0050.196
lastMcmc0.0010.0000.001
output0.1100.0070.117
ssStatistic1.0620.0341.096
studyCenter0.0650.0050.070
symbolsInteresting0.1540.0080.163
xde000
xmcmc0.0760.0040.081
xsScores0.0260.0030.029