Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:40:06 -0400 (Thu, 12 Apr 2018).
Package 272/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CODEX 1.10.0 Yuchao Jiang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | ![]() |
Package: CODEX |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.10.0.tar.gz |
StartedAt: 2018-04-12 02:02:06 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 02:06:31 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 264.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CODEX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CODEX.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CODEX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CODEX’ version ‘1.10.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘Rsamtools’ ‘GenomeInfoDb’ ‘BSgenome.Hsapiens.UCSC.hg19’ ‘IRanges’ ‘Biostrings’ ‘S4Vectors’ Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘CODEX’ 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 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 choiceofK: no visible global function definition for ‘pdf’ choiceofK: no visible global function definition for ‘par’ choiceofK: no visible global function definition for ‘plot’ choiceofK: no visible global function definition for ‘dev.off’ getbambed: no visible global function definition for ‘read.table’ normalize : <anonymous>: no visible global function definition for ‘smooth.spline’ normalize : <anonymous>: no visible global function definition for ‘predict’ normalize: no visible global function definition for ‘glm’ normalize: no visible binding for global variable ‘poisson’ normalize: no visible global function definition for ‘lm’ normalize2 : <anonymous>: no visible global function definition for ‘smooth.spline’ normalize2 : <anonymous>: no visible global function definition for ‘predict’ normalize2: no visible global function definition for ‘glm’ normalize2: no visible binding for global variable ‘poisson’ normalize2: no visible global function definition for ‘lm’ Undefined global functions or variables: dev.off glm lm par pdf plot poisson predict read.table smooth.spline Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "par", "plot") importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline") importFrom("utils", "read.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 sizes of PDF files under ‘inst/doc’ ... 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 normalize 28.456 0.599 29.514 normalize2 25.407 0.367 26.260 getcoverage 6.371 0.352 6.909 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.6-bioc/meat/CODEX.Rcheck/00check.log’ for details.
CODEX.Rcheck/00install.out
* installing *source* package ‘CODEX’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (CODEX)
CODEX.Rcheck/CODEX-Ex.timings
name | user | system | elapsed | |
bambedObjDemo | 0.001 | 0.001 | 0.002 | |
choiceofK | 0.031 | 0.006 | 0.037 | |
coverageObjDemo | 0.001 | 0.000 | 0.001 | |
gcDemo | 0.001 | 0.001 | 0.001 | |
getbambed | 0.018 | 0.003 | 0.022 | |
getcoverage | 6.371 | 0.352 | 6.909 | |
getgc | 1.529 | 0.077 | 1.650 | |
getmapp | 0.092 | 0.004 | 0.106 | |
mappDemo | 0.001 | 0.000 | 0.001 | |
mapp_ref | 0.076 | 0.000 | 0.077 | |
mappability | 0.001 | 0.000 | 0.002 | |
normObjDemo | 0.001 | 0.000 | 0.001 | |
normalize | 28.456 | 0.599 | 29.514 | |
normalize2 | 25.407 | 0.367 | 26.260 | |
qc | 0.041 | 0.001 | 0.043 | |
qcObjDemo | 0.001 | 0.000 | 0.001 | |
segment | 0.216 | 0.038 | 0.265 | |