##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings puma_3.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/puma.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘3.17.0’
* 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 44.595 1.255 46.280
hcomb 32.344 1.714 34.283
pumaDE 28.829 0.664 29.672
pumaCombImproved 18.158 0.820 19.130
pumaClustii 16.648 0.101 16.865
DEResult-class 11.303 0.408 12.878
pumaComb 11.120 0.178 11.406
plot-methods 9.107 0.203 9.422
pumaPCA 8.568 0.147 8.765
* 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.
* installing *source* package ‘puma’ ...
** 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 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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cregistration.c -o cregistration.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 donlp2.c -o donlp2.o
donlp2.c:270:5: warning: '/*' within block comment [-Wcomment]
/* bloc */
^
donlp2.c:470:26: warning: unused variable 'k' [-Wunused-variable]
static IINTEGER i,j,k;
^
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:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive
^
donlp2.c:2090:21: warning: unused variable 'eval_err' [-Wunused-variable]
static LLOGICAL eval_err;
^
donlp2.c:2076:22: warning: unused variable 'l' [-Wunused-variable]
static IINTEGER l,l0,i,j,k,csssig,csirup,csreg,cschgx;
^
donlp2.c:4127:5: warning: unused label 'L100' [-Wunused-label]
L100:
^˜˜˜˜
donlp2.c:4123:27: warning: unused variable 'term1' [-Wunused-variable]
static DDOUBLE term,term1;
^
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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c gme.c -o gme.o
gme.c:265:6: warning: unused variable 'niter' [-Wunused-variable]
int niter = 1, nx;
^
gme.c:268:6: warning: unused variable 'finishflag' [-Wunused-variable]
int finishflag = 1;
^
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: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: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: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:897:13: warning: unused variable 't1' [-Wunused-variable]
int i, j,t,t1;
^
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;
^
11 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 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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c newx.c -o newx.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 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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pumaclust_c.c -o pumaclust_c.o
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;
^
4 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 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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (puma)
