John D. Storey
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/snm |
| Branch: RELEASE_3_8 |
| Last Commit: d8ae381 |
| Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:27 -0400 (Sat, 13 Apr 2019).
| Package 1472/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| snm 1.30.0 John D. Storey
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: snm |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings snm_1.30.0.tar.gz |
| StartedAt: 2019-04-13 05:38:07 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:48:50 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 643.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: snm.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings snm_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/snm.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snm' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'snm' 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
buildBasisSplineMatrix : <anonymous>: no visible global function
definition for 'predict'
calcArrayEffects : <anonymous>: no visible global function definition
for 'predict'
edge.glr: no visible global function definition for 'pf'
edge.qvalue: no visible global function definition for 'smooth.spline'
edge.qvalue: no visible global function definition for 'predict'
fit.model: no visible binding for global variable 'weighted.mean'
fit.model: no visible global function definition for 'residuals'
getSpanningSet: no visible global function definition for 'quantile'
make.ref.model.matrices: no visible global function definition for
'model.matrix'
make.ref.model.matrices: no visible global function definition for
'as.formula'
make.snm.obj: no visible global function definition for 'model.matrix'
sim.doubleChannel: no visible global function definition for 'rchisq'
sim.doubleChannel: no visible global function definition for 'runif'
sim.doubleChannel: no visible global function definition for 'rnorm'
sim.doubleChannel: no visible binding for global variable 'rnorm'
sim.doubleChannel: no visible global function definition for
'model.matrix'
sim.function.var: no visible global function definition for
'model.matrix'
sim.intensity.dep: no visible global function definition for
'model.matrix'
sim.intensity.dep: no visible global function definition for 'predict'
sim.preProcessed: no visible global function definition for 'rchisq'
sim.preProcessed: no visible global function definition for 'runif'
sim.preProcessed: no visible global function definition for 'rnorm'
sim.preProcessed: no visible binding for global variable 'rnorm'
sim.preProcessed: no visible global function definition for
'model.matrix'
sim.probe.specific: no visible global function definition for
'model.matrix'
sim.refDesign: no visible global function definition for 'rchisq'
sim.refDesign: no visible global function definition for 'runif'
sim.refDesign: no visible binding for global variable 'rnorm'
sim.refDesign: no visible global function definition for 'rnorm'
sim.refDesign: no visible global function definition for 'model.matrix'
sim.singleChannel: no visible global function definition for 'rchisq'
sim.singleChannel: no visible global function definition for 'runif'
sim.singleChannel: no visible global function definition for 'rnorm'
sim.singleChannel: no visible binding for global variable 'rnorm'
sim.singleChannel: no visible global function definition for
'model.matrix'
snm.diagnostic.plot: no visible global function definition for 'par'
snm.diagnostic.plot: no visible global function definition for 'plot'
snm.diagnostic.plot: no visible global function definition for 'axis'
snm.diagnostic.plot : <anonymous>: no visible global function
definition for 'points'
snm.diagnostic.plot: no visible global function definition for 'hist'
snm.diagnostic.plot: no visible global function definition for 'abline'
snm.diagnostic.plot: no visible global function definition for 'mtext'
snm.diagnostic.plot: no visible global function definition for 'title'
snm.plot: no visible global function definition for 'model.matrix'
snm.plot: no visible global function definition for 'rainbow'
snm.plot: no visible global function definition for 'plot'
snm.plot: no visible global function definition for 'points'
snm.plot: no visible global function definition for 'par'
snm.plot: no visible global function definition for 'abline'
snm.plot: no visible global function definition for 'fitted'
snm.plot: no visible global function definition for 'hist'
snm.plot: no visible global function definition for 'mtext'
snm.plot: no visible global function definition for 'title'
Undefined global functions or variables:
abline as.formula axis fitted hist model.matrix mtext par pf plot
points predict quantile rainbow rchisq residuals rnorm runif
smooth.spline title weighted.mean
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
"plot", "points", "title")
importFrom("stats", "as.formula", "fitted", "model.matrix", "pf",
"predict", "quantile", "rchisq", "residuals", "rnorm",
"runif", "smooth.spline", "weighted.mean")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sim.refDesign 157.22 6.81 164.03
snm 112.94 8.08 121.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sim.refDesign 117.22 5.29 122.51
snm 103.87 1.77 105.67
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/snm.Rcheck/00check.log'
for details.
snm.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/snm_1.30.0.tar.gz && rm -rf snm.buildbin-libdir && mkdir snm.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snm.buildbin-libdir snm_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL snm_1.30.0.zip && rm snm_1.30.0.tar.gz snm_1.30.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 212k 100 212k 0 0 5647k 0 --:--:-- --:--:-- --:--:-- 6260k
install for i386
* installing *source* package 'snm' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'snm'
finding HTML links ... done
fitted.snm html
plot.snm html
sim.doubleChannel html
sim.preProcessed html
sim.refDesign html
sim.singleChannel html
snm-internal html
snm html
summary.snm html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'snm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snm' as snm_1.30.0.zip
* DONE (snm)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'snm' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
snm.Rcheck/examples_i386/snm-Ex.timings
|
snm.Rcheck/examples_x64/snm-Ex.timings
|