| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:32 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 | ||||
| Package 379/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cn.farms 1.50.0 (landing page) Andreas Mitterecker
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the cn.farms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cn.farms.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: cn.farms |
| Version: 1.50.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings cn.farms_1.50.0.tar.gz |
| StartedAt: 2023-11-02 09:23:25 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 09:28:26 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 301.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.farms.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings cn.farms_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/cn.farms.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.50.0’
* 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 ‘cn.farms’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 startup messages can be suppressed ... 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
calcDistance: no visible global function definition for ‘density’
callSummarizeH01: no visible binding for global variable ‘var’
callSummarizeH01: no visible global function definition for ‘rnorm’
createAnnotation: no visible global function definition for
‘installed.packages’
determineBaselineArray: no visible binding for global variable ‘median’
flcSnp6Std: no visible global function definition for ‘lowess’
flcSnp6Std: no visible global function definition for ‘approx’
flcSnp6StdH01: no visible global function definition for ‘lowess’
flcSnp6StdH01: no visible global function definition for ‘approx’
flcStd: no visible global function definition for ‘lowess’
flcStd: no visible global function definition for ‘approx’
flcStdH01: no visible global function definition for ‘lowess’
flcStdH01: no visible global function definition for ‘approx’
getProbePositionEffectDesignMatrix: no visible global function
definition for ‘head’
getVar: no visible global function definition for ‘getFromNamespace’
initializeBigMatrix: no visible global function definition for
‘isPackageLoaded’
normalizeAverage: no visible binding for global variable ‘median’
normalizeAverage: no visible global function definition for ‘median’
normalizeSorH01: no visible binding for global variable ‘pairs’
normalizeSorH01: no visible global function definition for ‘median’
plotDendrogram : colLab: no visible global function definition for
‘is.leaf’
plotDendrogram: no visible global function definition for
‘as.dendrogram’
plotDendrogram: no visible global function definition for ‘hclust’
plotDendrogram: no visible global function definition for
‘order.dendrogram’
plotDendrogram: no visible global function definition for ‘dendrapply’
plotDensity: no visible global function definition for ‘density’
plotDensity: no visible global function definition for ‘lines’
plotEvalIc: no visible global function definition for ‘rgb’
plotEvalIc: no visible global function definition for ‘rect’
plotEvalIc: no visible global function definition for ‘points’
plotEvalIc: no visible global function definition for ‘densCols’
plotEvalIc: no visible global function definition for ‘mtext’
plotRegions: no visible global function definition for ‘pdf’
plotRegions: no visible global function definition for ‘text’
plotRegions: no visible global function definition for ‘par’
plotRegions: no visible global function definition for ‘matplot’
plotRegions: no visible global function definition for ‘abline’
plotRegions: no visible global function definition for ‘matlines’
plotRegions: no visible global function definition for ‘legend’
plotRegions: no visible global function definition for ‘axis’
plotRegions: no visible global function definition for ‘nclass.Sturges’
plotRegions: no visible global function definition for ‘dev.off’
plotSmoothScatter: no visible global function definition for ‘pdf’
plotSmoothScatter: no visible global function definition for
‘smoothScatter’
plotSmoothScatter: no visible global function definition for ‘abline’
plotSmoothScatter: no visible global function definition for ‘loess’
plotSmoothScatter: no visible global function definition for ‘points’
plotSmoothScatter: no visible global function definition for ‘dev.off’
setVar: no visible global function definition for ‘assignInNamespace’
sfClusterSetupSPRNG: no visible global function definition for ‘runif’
sfExport: no visible global function definition for ‘getFromNamespace’
sfExportAll: no visible global function definition for ‘na.omit’
sfInit: no visible global function definition for ‘makeNWScluster’
sfInit: no visible global function definition for ‘packageDescription’
sfTest : testCalc1: no visible global function definition for ‘runif’
sfTest : testCalc2: no visible global function definition for ‘runif’
summarizeFarmsExact: no visible global function definition for ‘median’
summarizeFarmsExact: no visible binding for global variable ‘median’
summarizeFarmsExact: no visible global function definition for ‘pchisq’
summarizeFarmsExact2: no visible global function definition for
‘median’
summarizeFarmsExact2: no visible binding for global variable ‘median’
summarizeFarmsExact2: no visible global function definition for
‘pchisq’
summarizeFarmsExact3: no visible global function definition for
‘median’
summarizeFarmsExact3: no visible binding for global variable ‘median’
summarizeFarmsExact3: no visible global function definition for
‘pchisq’
summarizeFarmsGaussian: no visible global function definition for
‘median’
summarizeFarmsGaussian: no visible binding for global variable ‘median’
summarizeFarmsGaussian: no visible global function definition for ‘var’
summarizeFarmsStatistics: no visible binding for global variable
‘median’
summarizeFarmsStatistics: no visible global function definition for
‘median’
summarizeFarmsVariational: no visible binding for global variable
‘median’
summarizeFarmsVariational: no visible global function definition for
‘sd’
summarizeFarmsVariational: no visible global function definition for
‘median’
summarizeFarmsVariational: no visible global function definition for
‘var’
Undefined global functions or variables:
abline approx as.dendrogram assignInNamespace axis dendrapply
densCols density dev.off getFromNamespace hclust head
installed.packages is.leaf isPackageLoaded legend lines loess lowess
makeNWScluster matlines matplot median mtext na.omit nclass.Sturges
order.dendrogram packageDescription pairs par pchisq pdf points rect
rgb rnorm runif sd smoothScatter text var
Consider adding
importFrom("grDevices", "densCols", "dev.off", "nclass.Sturges", "pdf",
"rgb")
importFrom("graphics", "abline", "axis", "legend", "lines", "matlines",
"matplot", "mtext", "pairs", "par", "points", "rect",
"smoothScatter", "text")
importFrom("stats", "approx", "as.dendrogram", "dendrapply", "density",
"hclust", "is.leaf", "loess", "lowess", "median", "na.omit",
"order.dendrogram", "pchisq", "rnorm", "runif", "sd", "var")
importFrom("utils", "assignInNamespace", "getFromNamespace", "head",
"installed.packages", "packageDescription")
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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/cn.farms.Rcheck/00check.log’
for details.
cn.farms.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL cn.farms
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘cn.farms’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:6: warning: unused variable ‘method’ [-Wunused-variable]
442 | int method=0;
| ^~~~~~
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:387:28: warning: ‘I1right’ may be used uninitialized in this function [-Wmaybe-uninitialized]
387 | absMoment1=(I1right*leftMy+I1left*rightMy+2.0*I1left*I1right*leftSigma)/(I1left-I1right);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
laplace.cpp:367:9: warning: ‘I1left’ may be used uninitialized in this function [-Wmaybe-uninitialized]
367 | double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sparse_farms.c -o sparse_farms.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-cn.farms/00new/cn.farms/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cn.farms)
cn.farms.Rcheck/cn.farms-Ex.timings
| name | user | system | elapsed | |
| cn.farms | 0 | 0 | 0 | |
| combineData | 1.964 | 0.044 | 2.019 | |
| createAnnotation | 0 | 0 | 0 | |
| distributionDistance | 0.111 | 0.009 | 0.120 | |
| dnaCopySf | 0.107 | 0.000 | 0.110 | |
| fragLengCorr | 2.356 | 0.087 | 2.451 | |
| mlSummarization | 4.118 | 0.112 | 4.241 | |
| normalizeAverage | 0.001 | 0.000 | 0.002 | |
| normalizeCels | 0 | 0 | 0 | |
| normalizeNpData | 0.001 | 0.000 | 0.000 | |
| plotDendrogram | 0.116 | 0.004 | 0.119 | |
| plotDensity | 0.392 | 0.004 | 0.397 | |
| plotEvalIc | 0.270 | 0.012 | 0.285 | |
| plotRegions | 0.133 | 0.000 | 0.133 | |
| plotSmoothScatter | 0.297 | 0.004 | 0.301 | |
| plotViolines | 0.122 | 0.000 | 0.123 | |
| slSummarization | 3.364 | 0.036 | 3.405 | |
| sparseFarmsC | 0 | 0 | 0 | |
| summarizeFarmsExact | 0.003 | 0.002 | 0.005 | |
| summarizeFarmsExact2 | 0.005 | 0.000 | 0.005 | |
| summarizeFarmsExact3 | 0.005 | 0.000 | 0.005 | |
| summarizeFarmsGaussian | 0.002 | 0.000 | 0.002 | |
| summarizeFarmsMethods | 0.002 | 0.000 | 0.002 | |
| summarizeFarmsVariational | 0.005 | 0.000 | 0.005 | |
| summarizeWindowBps | 0.002 | 0.003 | 0.005 | |
| summarizeWindowMethods | 0.002 | 0.000 | 0.002 | |
| summarizeWindowStd | 0.003 | 0.000 | 0.003 | |