yeastCC 1.17.0
Sandrine Dudoit
| Snapshot Date: 2017-08-15 09:00:08 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/yeastCC | | Last Changed Rev: 4157 / Revision: 4227 | | Last Changed Date: 2017-04-24 16:19:55 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings yeastCC_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yeastCC/DESCRIPTION’ ... OK
* this is package ‘yeastCC’ version ‘1.17.0’
* 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 ‘yeastCC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found directory ‘R’ with no source files.
* 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
Error in tools:::.check_packages_used(package = "yeastCC") :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "yeastCC") :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in tools::checkReplaceFuns(package = "yeastCC") :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in tools::checkFF(package = "yeastCC", registration = FALSE, check_DUP = TRUE) :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Error in tools::codoc(package = "yeastCC") :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
Error in tools::codocClasses(package = "yeastCC") :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "yeastCC") :
directory '/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Warning: large data file saved inefficiently:
size ASCII compress
spYCCmeta.rda 430Kb FALSE none
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
breeden.rda 1.9Mb 1.5Mb xz
spYCCES.rda 757Kb 483Kb xz
spYCCmeta.rda 430Kb 55Kb xz
yeastCC.rda 1.5Mb 485Kb xz
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘CellCycle98.txt’, ‘CellCycle98.xls’, ‘KnownGenes.doc’,
‘KnownGenes.txt’, ‘Spellmanetal.pdf’, ‘consistentFHCRC.csv’,
‘createYeastCC.R’, ‘orf800.txt’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 6 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.6-data-experiment/meat/yeastCC.Rcheck/00check.log’
for details.