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BioC 3.2: CHECK report for cn.farms on oaxaca

This page was generated on 2016-04-23 10:25:06 -0700 (Sat, 23 Apr 2016).

Package 190/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.18.0
Andreas Mitterecker
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/cn.farms
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  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.farms
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.farms_1.18.0.tar.gz
StartedAt: 2016-04-22 22:51:52 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:54:40 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 167.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.farms_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/cn.farms.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 ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.18.0’
* 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 ‘cn.farms’ can be installed ... [16s/16s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initializeBigMatrix: no visible global function definition for
  ‘isPackageLoaded’
* 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 R/sysdata.rda ... 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 ... [18s/19s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck/00check.log’
for details.


cn.farms.Rcheck/00install.out:

* installing *source* package ‘cn.farms’ ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.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 laplace.cpp -o laplace.o
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:364:36: note: uninitialized use occurs here
        double I2left=(-leftMy/leftSigma)*I1left+I0left;
                                          ^˜˜˜˜˜
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:364:36: note: uninitialized use occurs here
        double I2left=(-leftMy/leftSigma)*I1left+I0left;
                                          ^˜˜˜˜˜
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:198:15: note: initialize the variable 'I1left' to silence this warning
        double I1left;
                     ^
                      = 0.0
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:365:39: note: uninitialized use occurs here
        double I2right=(-rightMy/rightSigma)*I1right+I0right;
                                             ^˜˜˜˜˜˜
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:365:39: note: uninitialized use occurs here
        double I2right=(-rightMy/rightSigma)*I1right+I0right;
                                             ^˜˜˜˜˜˜
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
        else if(argLeft >= 0.0 && argRight >= 0.0) {
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:199:16: note: initialize the variable 'I1right' to silence this warning
        double I1right;
                      ^
                       = 0.0
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
        int method=0;
            ^
laplace.cpp:23:11: warning: unused variable 'steps' [-Wunused-const-variable]
const int steps=30;
          ^
laplace.cpp:26:14: warning: unused variable 'integrationFailureFactor' [-Wunused-const-variable]
const double integrationFailureFactor=5.0;
             ^
laplace.cpp:27:14: warning: unused variable 'sigmaFactor' [-Wunused-const-variable]
const double sigmaFactor=0.1;
             ^
laplace.cpp:30:14: warning: unused variable 'Pi' [-Wunused-const-variable]
const double Pi=M_PI;
             ^
laplace.cpp:31:14: warning: unused variable 'E' [-Wunused-const-variable]
const double E=M_E;
             ^
laplace.cpp:34:14: warning: unused variable 'sqrt3' [-Wunused-const-variable]
const double sqrt3=1.7320508075688772935274463415058723669428052538104;
             ^
laplace.cpp:35:14: warning: unused variable 'sqrt2Pi' [-Wunused-const-variable]
const double sqrt2Pi=2.5066282746310005024157652848110452530069867406099;
             ^
12 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 sparse_farms.c -o sparse_farms.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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

cn.farms.Rcheck/cn.farms-Ex.timings:

nameusersystemelapsed
cn.farms0.0010.0000.001
combineData1.1550.0441.256
createAnnotation000
distributionDistance0.3310.0050.337
dnaCopySf0.1250.0020.127
fragLengCorr2.5390.0432.588
mlSummarization2.9420.1003.050
normalizeAverage0.0020.0000.002
normalizeCels0.0010.0000.000
normalizeNpData000
plotDendrogram0.2930.0070.301
plotDensity0.4010.0110.413
plotEvalIc0.3870.0120.425
plotRegions0.3530.0070.363
plotSmoothScatter0.3320.0140.354
plotViolines0.1520.0020.155
slSummarization2.8260.0383.071
sparseFarmsC0.0010.0000.001
summarizeFarmsExact0.0040.0010.005
summarizeFarmsExact20.0040.0010.006
summarizeFarmsExact30.0050.0010.007
summarizeFarmsGaussian0.0030.0010.003
summarizeFarmsMethods0.0030.0000.003
summarizeFarmsVariational0.0030.0010.004
summarizeWindowBps0.0070.0000.008
summarizeWindowMethods0.0020.0000.003
summarizeWindowStd0.0040.0000.005