Robert Gentleman
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/RBioinf |
| git_branch: RELEASE_3_14 |
| git_last_commit: e5acd0f |
| git_last_commit_date: 2021-10-26 11:52:12 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:10 -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 RBioinf package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBioinf.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 1534/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RBioinf 1.54.0 (landing page) Robert Gentleman
| 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: RBioinf |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RBioinf.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RBioinf_1.54.0.tar.gz |
| StartedAt: 2022-04-13 01:16:07 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:16:59 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 52.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RBioinf.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:RBioinf.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RBioinf_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RBioinf.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 'RBioinf/DESCRIPTION' ... OK
* this is package 'RBioinf' version '1.54.0'
* 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 whether package 'RBioinf' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.5Mb
sub-directories of 1Mb or more:
extdata 12.3Mb
* 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 ... NOTE
Packages in Depends field not imported from:
'graph' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'methods:::.getMethodsTable'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument
match of 'nr' to 'nrow'
class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument
match of 'nc' to 'ncol'
LPO: no visible global function definition for 'getClass'
OLDcplList: no visible global function definition for
'getAllSuperClasses'
OLDcplList: no visible global function definition for 'getClass'
S4Help: no visible global function definition for 'isClass'
S4Help: no visible global function definition for 'getAllSuperClasses'
S4Help: no visible global function definition for 'getClass'
S4Help: no visible global function definition for 'menu'
S4Help: no visible global function definition for 'isGeneric'
S4Help: no visible global function definition for 'getGeneric'
S4Help: no visible binding for global variable 'help'
candidateDirectSC: no visible global function definition for 'getClass'
class2Graph: no visible global function definition for 'is'
class2Graph: no visible global function definition for 'getClass'
class2Graph: no visible global function definition for
'getAllSuperClasses'
class2Graph: no visible global function definition for 'new'
class2Graph: no visible global function definition for 'as'
classList2Graph: no visible global function definition for 'join'
computeClassLinearization: no visible global function definition for
'getClass'
printWithNumbers: no visible global function definition for 'is'
subClassNames: no visible global function definition for 'isClassDef'
subClassNames: no visible global function definition for 'getClass'
superClassNames: no visible global function definition for 'isClassDef'
superClassNames: no visible global function definition for 'getClass'
superClasses: no visible global function definition for 'is'
traceMethods: no visible global function definition for 'isGeneric'
traceMethods: no visible global function definition for 'showMethods'
Undefined global functions or variables:
as getAllSuperClasses getClass getGeneric help is isClass isClassDef
isGeneric join menu new showMethods
Consider adding
importFrom("methods", "as", "getAllSuperClasses", "getClass",
"getGeneric", "is", "isClass", "isClassDef", "isGeneric",
"new", "showMethods")
importFrom("utils", "help", "menu")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RBioinf/libs/i386/RBioinf.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RBioinf/libs/x64/RBioinf.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/RBioinf.Rcheck/00check.log'
for details.
RBioinf.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/RBioinf_1.54.0.tar.gz && rm -rf RBioinf.buildbin-libdir && mkdir RBioinf.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RBioinf.buildbin-libdir RBioinf_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RBioinf_1.54.0.zip && rm RBioinf_1.54.0.tar.gz RBioinf_1.54.0.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
12 3430k 12 426k 0 0 875k 0 0:00:03 --:--:-- 0:00:03 874k
63 3430k 63 2175k 0 0 1464k 0 0:00:02 0:00:01 0:00:01 1464k
100 3430k 100 3430k 0 0 1714k 0 0:00:02 0:00:02 --:--:-- 1715k
install for i386
* installing *source* package 'RBioinf' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rand.c -o rand.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o RBioinf.dll tmp.def Rinit.o rand.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RBioinf.buildbin-libdir/00LOCK-RBioinf/00new/RBioinf/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RBioinf'
finding HTML links ... done
Rcal html
S4Help html
asSimpleVector html
classList2Graph html
computeClassLinearization html
printWithNumbers html
randDNA html
simplePVect html
simpleRand html
simpleSort html
subClassNames html
superClasses html
traceMethods 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 'RBioinf' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rand.c -o rand.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o RBioinf.dll tmp.def Rinit.o rand.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RBioinf.buildbin-libdir/RBioinf/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RBioinf' as RBioinf_1.54.0.zip
* DONE (RBioinf)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RBioinf' successfully unpacked and MD5 sums checked
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RBioinf.Rcheck/examples_i386/RBioinf-Ex.timings
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RBioinf.Rcheck/examples_x64/RBioinf-Ex.timings
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