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BioC 3.5: CHECK report for puma on veracruz2

This page was generated on 2017-08-16 13:28:00 -0400 (Wed, 16 Aug 2017).

Package 1029/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
puma 3.18.0
Xuejun Liu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/puma
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: puma
Version: 3.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings puma_3.18.0.tar.gz
StartedAt: 2017-08-16 06:49:39 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:56:03 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 383.2 seconds
RetCode: 0
Status:  OK 
CheckDir: puma.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings puma_3.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/puma.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘3.18.0’
* 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 ‘puma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘oligoClasses’
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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘ROCR’ ‘limma’ ‘pumadata’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
  ‘affy:::mm’ ‘affy:::pm’ ‘affy:::probeNames’ ‘oligo:::mm’ ‘oligo:::pm’
  ‘oligo:::probeNames’ ‘oligo:::rma’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMmmgmos: no visible binding for global variable ‘median’
PMmmgmos: no visible global function definition for ‘description’
calcAUC: no visible global function definition for ‘prediction’
calcAUC: no visible global function definition for ‘performance’
calculateLimma: no visible global function definition for ‘lmFit’
calculateLimma: no visible global function definition for
  ‘contrasts.fit’
calculateLimma: no visible global function definition for ‘eBayes’
calculateTtest : <anonymous>: no visible global function definition for
  ‘t.test’
clusterApplyLBDots : submit: no visible global function definition for
  ‘sendCall’
clusterApplyLBDots: no visible global function definition for
  ‘recvOneResult’
clusterNormE: no visible global function definition for ‘var’
clusterNormVar: no visible global function definition for ‘var’
compareLimmapumaDE: no visible global function definition for ‘pdf’
compareLimmapumaDE: no visible global function definition for ‘dev.off’
compareLimmapumaDE: no visible global function definition for ‘par’
compareLimmapumaDE: no visible global function definition for
  ‘vennDiagram’
createDesignMatrix: no visible global function definition for
  ‘model.matrix’
erfc: no visible global function definition for ‘pnorm’
gmhta: no visible global function definition for ‘clusterEvalQ’
gmhta: no visible global function definition for ‘data’
gmhta: no visible global function definition for ‘clusterApplyLB’
gmhta: no visible global function definition for ‘stopCluster’
gmhta: no visible binding for global variable ‘median’
gmoExon: no visible global function definition for ‘clusterEvalQ’
gmoExon: no visible global function definition for ‘data’
gmoExon: no visible global function definition for ‘clusterApplyLB’
gmoExon: no visible global function definition for ‘stopCluster’
gmoExon: no visible binding for global variable ‘median’
igmoExon: no visible global function definition for ‘clusterEvalQ’
igmoExon: no visible global function definition for ‘read.table’
igmoExon: no visible global function definition for ‘data’
igmoExon: no visible global function definition for ‘clusterApplyLB’
igmoExon: no visible global function definition for ‘stopCluster’
igmoExon: no visible binding for global variable ‘median’
just.mgmos: no visible binding for global variable ‘median’
just.mmgmos: no visible binding for global variable ‘median’
legend2: no visible global function definition for ‘par’
legend2: no visible global function definition for ‘xy.coords’
legend2 : rect2: no visible global function definition for ‘rect’
legend2 : segments2: no visible global function definition for
  ‘segments’
legend2 : points2: no visible global function definition for ‘points’
legend2 : text2: no visible global function definition for ‘text’
legend2: no visible global function definition for ‘strwidth’
legend2: no visible global function definition for ‘xinch’
legend2: no visible global function definition for ‘yinch’
legend2: no visible global function definition for ‘strheight’
matrixDistance: no visible global function definition for ‘dist’
mgmos: no visible binding for global variable ‘median’
mmgmos: no visible binding for global variable ‘median’
plot.pumaPCARes: no visible global function definition for ‘plot’
plot.pumaPCARes: no visible global function definition for ‘text’
plot.pumaPCARes: no visible global function definition for ‘legend’
plotErrorBars: no visible global function definition for ‘qnorm’
plotErrorBars: no visible global function definition for ‘par’
plotErrorBars: no visible global function definition for ‘even’
plotErrorBars: no visible global function definition for ‘odd’
plotErrorBars: no visible global function definition for ‘plot’
plotErrorBars: no visible global function definition for ‘arrows’
plotErrorBars: no visible global function definition for ‘points’
plotErrorBars: no visible global function definition for ‘axis’
plotErrorBars: no visible global function definition for ‘title’
plotHistTwoClasses: no visible global function definition for ‘axis’
plotHistTwoClasses: no visible global function definition for ‘box’
plotROC: no visible global function definition for ‘prediction’
plotROC: no visible global function definition for ‘performance’
plotROC: no visible global function definition for ‘plot’
plotWhiskers: no visible global function definition for ‘plot’
plotWhiskers: no visible global function definition for ‘segments’
plotWhiskers: no visible global function definition for ‘qnorm’
plotWhiskers: no visible global function definition for ‘points’
plotWhiskers: no visible global function definition for ‘abline’
pumaClust: no visible global function definition for ‘read.csv’
pumaClust: no visible global function definition for ‘kmeans’
pumaClust: no visible global function definition for ‘cov’
pumaClustii: no visible global function definition for ‘read.csv’
pumaClustii: no visible global function definition for ‘cov’
pumaComb: no visible global function definition for ‘getMPIcluster’
pumaComb: no visible global function definition for ‘makeCluster’
pumaComb: no visible global function definition for ‘clusterEvalQ’
pumaComb: no visible global function definition for ‘clusterApplyLB’
pumaCombImproved: no visible global function definition for
  ‘getMPIcluster’
pumaCombImproved: no visible global function definition for
  ‘makeCluster’
pumaCombImproved: no visible global function definition for
  ‘clusterEvalQ’
pumaCombImproved: no visible global function definition for
  ‘clusterApplyLB’
pumaFull: no visible global function definition for ‘pdf’
pumaFull: no visible global function definition for ‘par’
pumaFull: no visible global function definition for ‘plot’
pumaFull: no visible global function definition for ‘prcomp’
pumaFull: no visible global function definition for ‘dev.off’
pumaNormalize: no visible binding for global variable ‘median’
pumaPCA: no visible global function definition for ‘prcomp’
pumaPCA: no visible global function definition for ‘rnorm’
pumaPCA: no visible global function definition for ‘optimise’
pumaPCA: no visible global function definition for ‘optim’
pumaPCA: no visible global function definition for ‘par’
pumaPCA: no visible global function definition for ‘plot’
pumaPCARemoveRedundancy: no visible global function definition for
  ‘dist’
write.reslts,DEResult: no visible global function definition for
  ‘write.table’
write.reslts,ExpressionSet: no visible global function definition for
  ‘write.table’
write.reslts,exprReslt: no visible global function definition for
  ‘write.table’
write.reslts,pumaPCARes: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline arrows axis box clusterApplyLB clusterEvalQ contrasts.fit cov
  data description dev.off dist eBayes even getMPIcluster kmeans legend
  lmFit makeCluster median model.matrix odd optim optimise par pdf
  performance plot pnorm points prcomp prediction qnorm read.csv
  read.table rect recvOneResult rnorm segments sendCall stopCluster
  strheight strwidth t.test text title var vennDiagram write.table
  xinch xy.coords yinch
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "xy.coords")
  importFrom("graphics", "abline", "arrows", "axis", "box", "legend",
             "par", "plot", "points", "rect", "segments", "strheight",
             "strwidth", "text", "title", "xinch", "yinch")
  importFrom("stats", "cov", "dist", "kmeans", "median", "model.matrix",
             "optim", "optimise", "pnorm", "prcomp", "qnorm", "rnorm",
             "t.test", "var")
  importFrom("utils", "data", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
puma-package     41.318  1.557  43.983
hcomb            31.963  2.978  35.972
pumaDE           27.815  1.415  30.057
pumaCombImproved 16.924  1.221  18.629
pumaClustii      14.794  0.078  15.294
DEResult-class   10.998  0.280  12.409
pumaComb         10.702  0.336  11.274
plot-methods      7.377  0.170   7.789
pumaPCA           7.028  0.104   7.383
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/puma.Rcheck/00check.log’
for details.


puma.Rcheck/00install.out:

* installing *source* package ‘puma’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
PMmultimgmos.c:425:23: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER i,j;
                      ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cregistration.c -o cregistration.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c donlp2.c -o donlp2.o
donlp2.c:270:5: warning: '/*' within block comment [-Wcomment]
    /*  bloc                                                                  */
    ^
donlp2.c:471:39: warning: unused variable 'gxi' [-Wunused-variable]
    static DDOUBLE   tol1 ,bd0,infiny,gxi,hxi,term;
                                      ^
donlp2.c:471:43: warning: unused variable 'hxi' [-Wunused-variable]
    static DDOUBLE   tol1 ,bd0,infiny,gxi,hxi,term;
                                          ^
donlp2.c:471:28: warning: unused variable 'bd0' [-Wunused-variable]
    static DDOUBLE   tol1 ,bd0,infiny,gxi,hxi,term;
                           ^
donlp2.c:470:26: warning: unused variable 'k' [-Wunused-variable]
    static IINTEGER  i,j,k;
                         ^
donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive  
^
donlp2.c:2076:22: warning: unused variable 'l' [-Wunused-variable]
    static IINTEGER  l,l0,i,j,k,csssig,csirup,csreg,cschgx;
                     ^
donlp2.c:2090:21: warning: unused variable 'eval_err' [-Wunused-variable]
    static LLOGICAL eval_err;
                    ^
donlp2.c:4123:27: warning: unused variable 'term1' [-Wunused-variable]
    static DDOUBLE   term,term1;
                          ^
donlp2.c:4127:5: warning: unused label 'L100' [-Wunused-label]
    L100:
    ^˜˜˜˜
donlp2.c:4412:24: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER  i,j;
                       ^
donlp2.c:5027:28: warning: unused variable 'l' [-Wunused-variable]
    static IINTEGER  i,j,k,l,i1,icur,ipiv;
                           ^
donlp2.c:5755:48: warning: unused variable 'term2' [-Wunused-variable]
                    su1,su2,condr,infiny,term1,term2,
                                               ^
donlp2.c:6418:9: warning: unused label 'L500' [-Wunused-label]
        L500:
        ^˜˜˜˜
donlp2.c:7153:5: warning: unused label 'L20' [-Wunused-label]
    L20:
    ^˜˜˜
donlp2.c:7878:16: warning: unused variable 'j' [-Wunused-variable]
    IINTEGER i,j;
               ^
donlp2.c:7916:14: warning: unused variable 'i' [-Wunused-variable]
    IINTEGER i;
             ^
donlp2.c:8009:16: warning: unused variable 'j' [-Wunused-variable]
    IINTEGER i,j;
               ^
donlp2.c:8044:14: warning: unused variable 'i' [-Wunused-variable]
    IINTEGER i;
             ^
donlp2.c:8141:16: warning: unused variable 'j' [-Wunused-variable]
    IINTEGER i,j;
               ^
donlp2.c:8177:14: warning: unused variable 'i' [-Wunused-variable]
    IINTEGER i;
             ^
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gme.c -o gme.o
gme.c:268:6: warning: unused variable 'finishflag' [-Wunused-variable]
        int finishflag = 1;
            ^
gme.c:265:6: warning: unused variable 'niter' [-Wunused-variable]
        int niter = 1, nx;
            ^
gme.c:349:10: warning: unused variable 'alphai' [-Wunused-variable]
        double  alphai, c, d,alpha_temp,kk_gene;
                ^
gme.c:354:9: warning: unused variable 'xxx' [-Wunused-variable]
    int xxx=(2+in_param->num_prctile)*in_param->numofgenes*in_param->chips;
        ^
gme.c:349:23: warning: unused variable 'alpha_temp' [-Wunused-variable]
        double  alphai, c, d,alpha_temp,kk_gene;
                             ^
gme.c:347:20: warning: unused variable 'px' [-Wunused-variable]
        int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
                          ^
gme.c:347:18: warning: unused variable 'q' [-Wunused-variable]
        int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
                        ^
gme.c:347:15: warning: unused variable 'k' [-Wunused-variable]
        int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
                     ^
gme.c:894:10: warning: unused variable 'res_isoform' [-Wunused-variable]
    SEXP res_isoform=NULL;
         ^
gme.c:897:11: warning: unused variable 't' [-Wunused-variable]
        int i, j,t,t1;
                 ^
gme.c:897:13: warning: unused variable 't1' [-Wunused-variable]
        int i, j,t,t1;
                   ^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ipplr_c.c -o ipplr_c.o
ipplr_c.c:255:114: warning: '&&' within '||' [-Wlogical-op-parentheses]
                   while(fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps||fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps&&n<2000)
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ipplr_c.c:255:114: note: place parentheses around the '&&' expression to silence this warning
                   while(fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps||fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps&&n<2000)
                                                                                                                               ^
                                                                            (                                                          )
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c multimgmos.c -o multimgmos.o
multimgmos.c:264:8: warning: unused variable 'Rf_pf' [-Wunused-variable]
        FILE *pf=NULL;
              ^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:285:13: note: expanded from macro 'pf'
#define pf              Rf_pf
                        ^
multimgmos.c:660:23: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER i,j;
                      ^
multimgmos.c:773:9: warning: unused variable 's5' [-Wunused-variable]
        double s5[MAX_NUM_PROBE]={0.0};
               ^
multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4;
                                                                                                     ^˜˜
                                                                                                     {  }
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c newx.c -o newx.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pplr_c.c -o pplr_c.o
pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable]
        double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
                                                                   ^
pplr_c.c:442:38: warning: unused variable 'var_c' [-Wunused-variable]
    double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
                                     ^
pplr_c.c:444:35: warning: unused variable 'lam_temp' [-Wunused-variable]
    double mu_temp[MAX_NUM_COND], lam_temp[MAX_NUM_COND];
                                  ^
pplr_c.c:444:12: warning: unused variable 'mu_temp' [-Wunused-variable]
    double mu_temp[MAX_NUM_COND], lam_temp[MAX_NUM_COND];
           ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pumaclust_c.c -o pumaclust_c.o
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^
pumaclust_c.c:181:24: note: use function 'fabs' instead
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^˜˜
                              fabs
pumaclust_c.c:384:41: warning: unused variable 'var_temp' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
                                               ^
pumaclust_c.c:384:30: warning: unused variable 'expr_temp' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
                                    ^
pumaclust_c.c:384:13: warning: unused variable 't2' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
                   ^
pumaclust_c.c:384:9: warning: unused variable 't1' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
               ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pumaclustii_c.c -o pumaclustii_c.o
pumaclustii_c.c:972:21: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER j;
                    ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c user_eval.c -o user_eval.o
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 puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/puma.Rcheck/puma/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (puma)

puma.Rcheck/puma-Ex.timings:

nameusersystemelapsed
DEResult-class10.998 0.28012.409
PMmmgmos0.0000.0000.001
bcomb0.2060.0260.240
calcAUC0.3820.0470.434
calculateFC3.1240.0543.247
calculateLimma2.1280.0352.224
calculateTtest0.0900.0000.092
clusterNormE0.0440.0030.047
clusterNormVar0.0520.0050.059
createContrastMatrix1.1210.0381.179
createDesignMatrix1.0130.0151.058
erfc0.0000.0000.001
exprReslt-class0.8540.0280.899
gmhta0.0000.0000.001
gmoExon0.0010.0010.001
hcomb31.963 2.97835.972
igmoExon0.0000.0000.001
legend20.0050.0010.007
license.puma0.0020.0000.002
matrixDistance0.0010.0010.002
mgmos0.0000.0000.001
mmgmos0.0010.0000.000
normalisation.gs0.0250.0060.031
numFP0.0150.0010.016
numOfFactorsToUse0.2730.0090.292
numTP0.0170.0010.018
orig_pplr0.1870.0120.202
plot-methods7.3770.1707.789
plotErrorBars0.2970.0120.319
plotHistTwoClasses0.0100.0010.012
plotROC0.5010.0020.513
pplr0.2330.0090.256
puma-package41.318 1.55743.983
pumaClustii14.794 0.07815.294
pumaComb10.702 0.33611.274
pumaCombImproved16.924 1.22118.629
pumaDE27.815 1.41530.057
pumaFull0.0010.0000.001
pumaNormalize0.3260.0160.356
pumaPCA7.0280.1047.383
pumaclust1.3290.0091.393
removeUninformativeFactors0.0410.0000.041