eiR 1.16.2
Thomas Girke
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/eiR | | Branch: RELEASE_3_5 | | Last Commit: 9730931 | | Last Changed Date: 2017-09-07 13:16:53 -0400 (Thu, 07 Sep 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings eiR_1.16.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/eiR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eiR’ version ‘1.16.2’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘eiR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘ChemmineR’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘RCurl’ ‘RUnit’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
IddbVsIddbDist : process : <anonymous> : <anonymous>: no visible global
function definition for ‘read.table’
checkEmbedding: no visible global function definition for ‘head’
eiMakeDb: no visible global function definition for ‘str’
eiMakeDb: no visible global function definition for ‘read.table’
eiMakeDb: no visible global function definition for ‘cmdscale’
eiMakeDb: no visible global function definition for ‘write.table’
eiPerformanceTest: no visible global function definition for
‘write.table’
embedFromRefs: no visible global function definition for ‘read.table’
getCoords: no visible global function definition for ‘read.table’
getEmbeddedDescriptors: no visible global function definition for
‘aggregate’
insertEmbeddedDescriptors: no visible global function definition for
‘postgresqlWriteTable’
insertEmbeddedDescriptorsByCompoundId: no visible global function
definition for ‘postgresqlWriteTable’
insertGroupMembers: no visible global function definition for
‘postgresqlWriteTable’
newEmbed: no visible global function definition for ‘optim’
toFile : write: no visible global function definition for ‘write.table’
toFile : writePart: no visible global function definition for
‘write.table’
writeIddbFile: no visible global function definition for ‘write.table’
Undefined global functions or variables:
aggregate cmdscale head optim postgresqlWriteTable read.table str
write.table
Consider adding
importFrom("stats", "aggregate", "cmdscale", "optim")
importFrom("utils", "head", "read.table", "str", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
eiPerformanceTest 4.218 1.709 6.664
eiAdd 4.714 1.211 6.519
eiCluster 3.602 1.741 6.118
eiQuery 2.799 1.664 5.101
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/eiR.Rcheck/00check.log’
for details.
* installing *source* package ‘eiR’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c optimFunctions.cc -o optimFunctions.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 eiR.so optimFunctions.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/eiR.Rcheck/eiR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eiR)