Package: SAGx

Version: 1.60.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SAGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SAGx_1.60.0.tar.gz

StartedAt: 2020-04-15 05:25:32 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:26:48 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 76.2 seconds

RetCode: 0

Status:  OK

CheckDir: SAGx.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:SAGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SAGx_1.60.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SAGx.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAGx’ version ‘1.60.0’
* 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 ‘SAGx’ 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘methods’ ‘stats’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SAGx/R/internal.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

Fstat: no visible binding for global variable ‘M’
GSEA.mean.t: no visible binding for global variable ‘samroc.res’
GSEA.mean.t: no visible binding for global variable ‘kegg’
GSEA.mean.t : maxmeanf: no visible binding for global variable
  ‘plustat’
R2BASE: no visible binding for global variable ‘clingen’
R2BASE: no visible binding for global variable ‘AZID’
R2BASE: no visible binding for global variable ‘dats’
R2BASE: no visible binding for global variable ‘annots’
R2BASE: no visible global function definition for ‘write.table’
R2mim: no visible binding for global variable ‘inm’
R2mim: no visible global function definition for ‘write.table’
Xprep: no visible binding for global variable ‘M’
Xprep.resid: no visible binding for global variable ‘M’
clin2mim: no visible binding for global variable ‘dbs’
clin2mim: no visible binding for global variable ‘clinical’
clin2mim: no visible global function definition for ‘write.table’
estimatep0: no visible binding for global variable ‘pp’
fetchSignal: no visible global function definition for ‘sqlQuery’
fp.fn: no visible binding for global variable ‘pvals’
gap: no visible binding for global variable ‘swiss’
gap: no visible binding for global variable ‘g’
list.experiments: no visible global function definition for ‘sqlQuery’
mat2TeX: no visible global function definition for ‘errif’
myclus: no visible binding for global variable ‘swiss’
p0.mom: no visible binding for global variable ‘pvalues’
p0.mom: no visible global function definition for ‘hist’
pava.fdr: no visible binding for global variable ‘pvalues’
rank.genes: no visible binding for global variable ‘indats’
rank.trend: no visible binding for global variable ‘x’
rsd.test: no visible binding for global variable ‘x’
rsd.test: no visible binding for global variable ‘y’
samrocN: no visible binding for global variable ‘M’
samrocNboot: no visible binding for global variable ‘M’
plot,samroc.result-ANY : plot.samroc.result: no visible global function
  definition for ‘lines’
plot,samroc.result-ANY : plot.samroc.result: no visible global function
  definition for ‘legend’
Undefined global functions or variables:
  AZID M annots clingen clinical dats dbs errif g hist indats inm kegg
  legend lines plustat pp pvals pvalues samroc.res sqlQuery swiss
  write.table x y
Consider adding
  importFrom("datasets", "swiss")
  importFrom("graphics", "hist", "legend", "lines")
  importFrom("utils", "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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/SAGx/libs/SAGx.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/SAGx.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 SAGx
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SAGx’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c minigsea.c -o minigsea.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c newboot.c -o newboot.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c samrocNboot.c -o samrocNboot.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 SAGx.so minigsea.o newboot.o samrocNboot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-SAGx/00new/SAGx/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAGx)

name	user	system	elapsed
Fstat	0.017	0.001	0.019
JT.test	0.006	0.000	0.007
fetchSignal	0	0	0
firstpass	0	0	0
gap	1.747	0.038	1.790
list.experiments	0	0	0
myclus	1.789	0.016	2.000
outlier	0.000	0.000	0.001
pava	0.001	0.000	0.001
rank.trend	0.002	0.001	0.003
samrocnboot	2.737	0.124	2.883
union.of.pways	0.001	0.000	0.001