Yuchao Jiang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/CODEX |
| git_branch: RELEASE_3_14 |
| git_last_commit: 729fd10 |
| git_last_commit_date: 2021-10-26 12:18:14 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:22 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CODEX package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CODEX.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 366/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CODEX 1.26.0 (landing page) Yuchao Jiang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CODEX |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CODEX_1.26.0.tar.gz |
| StartedAt: 2022-04-12 17:39:27 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:46:26 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 418.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CODEX.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CODEX_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CODEX.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CODEX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CODEX' version '1.26.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
choiceofK: no visible global function definition for 'pdf'
choiceofK: no visible global function definition for 'par'
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 poisson predict read.table smooth.spline
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "par")
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normalize2 20.97 0.06 21.03
normalize 20.82 0.03 20.84
getcoverage 19.08 0.47 54.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normalize 23.82 0.00 23.81
normalize2 21.12 0.02 21.14
getcoverage 9.81 0.31 10.12
* 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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/CODEX.Rcheck/00check.log'
for details.
CODEX.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CODEX_1.26.0.tar.gz && rm -rf CODEX.buildbin-libdir && mkdir CODEX.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CODEX.buildbin-libdir CODEX_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CODEX_1.26.0.zip && rm CODEX_1.26.0.tar.gz CODEX_1.26.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
93 734k 93 684k 0 0 872k 0 --:--:-- --:--:-- --:--:-- 872k
100 734k 100 734k 0 0 894k 0 --:--:-- --:--:-- --:--:-- 894k
install for i386
* installing *source* package 'CODEX' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CODEX'
finding HTML links ... done
CODEX-package html
bambedObjDemo html
choiceofK html
coverageObjDemo html
gcDemo html
getbambed html
getcoverage html
getgc html
getmapp html
mappDemo html
mapp_ref html
mappability html
normObjDemo html
normalize html
normalize2 html
qc html
qcObjDemo html
segment html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CODEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CODEX' as CODEX_1.26.0.zip
* DONE (CODEX)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CODEX' successfully unpacked and MD5 sums checked
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CODEX.Rcheck/examples_i386/CODEX-Ex.timings
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CODEX.Rcheck/examples_x64/CODEX-Ex.timings
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