Package: dexus

Version: 1.22.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dexus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dexus_1.22.1.tar.gz

StartedAt: 2019-04-15 23:29:46 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:30:37 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 51.1 seconds

RetCode: 0

Status:  OK

CheckDir: dexus.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dexus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dexus_1.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/dexus.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dexus’ version ‘1.22.1’
* 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 ‘dexus’ can be installed ... 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 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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-3.8-bioc/meat/dexus.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dexus
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘dexus’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dexus.cpp -o dexus.o
dexus.cpp:136:15: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((innerCyc==maxInnerCyc))
             ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
dexus.cpp:136:15: note: remove extraneous parentheses around the comparison to silence this warning
        if ((innerCyc==maxInnerCyc))
            ˜        ^            ˜
dexus.cpp:136:15: note: use '=' to turn this equality comparison into an assignment
        if ((innerCyc==maxInnerCyc))
                     ^˜
                     =
dexus.cpp:193:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
dexus.cpp:575:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
3 warnings 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 dexus.so dexus.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/dexus/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dexus)

name	user	system	elapsed
DEXUSResult-class	0.003	0.001	0.003
DEXUSResult-subset	1.565	0.080	1.666
INI	1.303	0.034	1.352
INIThreshold-set	0.722	0.017	0.746
accessors	0.759	0.037	0.800
dexss	1.352	0.043	1.404
dexus	0.767	0.020	0.799
dexus.parallel	0.852	0.028	0.892
getSizeNB	0.001	0.000	0.001
normalizeData	0.876	0.054	0.944
plot	1.295	0.050	1.360
sort	1.278	0.020	1.315