puma 3.25.0
Xuejun Liu
| Snapshot Date: 2019-03-17 17:01:51 -0400 (Sun, 17 Mar 2019) |
| URL: https://git.bioconductor.org/packages/puma |
| Branch: master |
| Last Commit: 2c019c5 |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:puma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings puma_3.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/puma.Rcheck’
* using R Under development (unstable) (2019-01-22 r76000)
* 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 ‘3.25.0’
* 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 ... WARNING
Found the following significant warnings:
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
The prototype for class “exprReslt” has undefined slot(s): 'exprs', 'se.exprs', 'description', 'notes', 'cdfName', 'nrow', 'ncol'
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/puma.Rcheck/00install.out’ for details.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.pumaPCARes
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... NOTE
Note: information on .o files is not available
* 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 52.768 3.145 55.968
hcomb 36.456 4.181 40.648
pumaDE 33.604 1.821 35.442
pumaCombImproved 20.303 1.466 21.774
pumaClustii 19.024 0.170 19.202
DEResult-class 13.099 0.701 13.809
pumaComb 12.739 0.463 13.204
plot-methods 11.982 0.550 12.536
pumaPCA 11.683 0.349 12.036
* 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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/puma.Rcheck/00check.log’
for details.
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL puma
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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:470:26: warning: unused variable 'k' [-Wunused-variable]
static IINTEGER i,j,k;
^
donlp2.c:471:43: warning: unused variable 'hxi' [-Wunused-variable]
static DDOUBLE tol1 ,bd0,infiny,gxi,hxi,term;
^
donlp2.c:471:39: warning: unused variable 'gxi' [-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: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: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 -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: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:347:20: 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: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:349:10: warning: unused variable 'alphai' [-Wunused-variable]
double alphai, c, d,alpha_temp,kk_gene;
^
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:269:13: 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:384:30: 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:384:41: warning: unused variable 'var_temp' [-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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/puma/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Warning in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, :
The prototype for class “exprReslt” has undefined slot(s): 'exprs', 'se.exprs', 'description', 'notes', 'cdfName', 'nrow', 'ncol'
** help
*** installing help indices
** building package indices
** installing vignettes
‘puma.Rnw’ using ‘UTF-8’
** testing if installed package can be loaded
* DONE (puma)