| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:12 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE CALIB PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 220/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Hui Zhao
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK |
| Package: CALIB |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CALIB.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CALIB_1.54.0.tar.gz |
| StartedAt: 2020-10-17 02:10:31 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:12:23 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 112.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CALIB.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CALIB.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CALIB_1.54.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' 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 'CALIB' can be installed ... WARNING
Found the following significant warnings:
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotNormalizedData.Rd:49: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeCI.Rd:68: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeCI.Rd:95: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeHI.Rd:69: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeHI.Rd:91: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeRG.Rd:90: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeSpotError.Rd:55: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'limma' 'methods'
A package should be listed in only one of these fields.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
[.ParameterList [.RGList_CALIB [.SpikeList cbind.ParameterList
cbind.RGList_CALIB cbind.SpikeList dim.RGList_CALIB dim.SpikeList
dimnames.RGList_CALIB dimnames.SpikeList length.RGList_CALIB
length.SpikeList merge.RGList_CALIB merge.SpikeList
rbind.RGList_CALIB rbind.SpikeList
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
read.rg: warning in scan(fullname, what = "", sep = sep, quote = quote,
skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE): partial
argument match of 'allowEscape' to 'allowEscapes'
getColClasses: no visible global function definition for 'namesInFun'
plotSpikeCI: no visible binding for global variable 'otherindex'
read.rg: no visible global function definition for 'readBlueFuseHeader'
read.spike: no visible binding for global variable 'files'
Undefined global functions or variables:
files namesInFun otherindex readBlueFuseHeader
* 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 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-3.11-bioc/R/library/CALIB/libs/i386/CALIB.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/CALIB/libs/x64/CALIB.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (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' ... ERROR
Running examples in 'CALIB-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: subsetting
> ### Title: Subset of RGList\_CALIB, SpikeList or ParameterList object
> ### Aliases: [.RGList_CALIB [.SpikeList [.ParameterList
> ### Keywords: array
>
> ### ** Examples
>
>
> # for RGList_CALIB
> R <- G <- matrix(1:8,4,2)
> rownames(R) <- rownames(G) <- c("g1","g2","g3","g4")
> colnames(R) <- colnames(G) <- c("a1","a2")
> RG <- new("RGList_CALIB",list(R=R,G=G))
>
> RG[1:2,]
Error in RG[1:2, ] : incorrect number of dimensions
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'CALIB-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: subsetting
> ### Title: Subset of RGList\_CALIB, SpikeList or ParameterList object
> ### Aliases: [.RGList_CALIB [.SpikeList [.ParameterList
> ### Keywords: array
>
> ### ** Examples
>
>
> # for RGList_CALIB
> R <- G <- matrix(1:8,4,2)
> rownames(R) <- rownames(G) <- c("g1","g2","g3","g4")
> colnames(R) <- colnames(G) <- c("a1","a2")
> RG <- new("RGList_CALIB",list(R=R,G=G))
>
> RG[1:2,]
Error in RG[1:2, ] : incorrect number of dimensions
Execution halted
* 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 ERRORs, 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.Rcheck/00check.log'
for details.
CALIB.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CALIB_1.54.0.tar.gz && rm -rf CALIB.buildbin-libdir && mkdir CALIB.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CALIB.buildbin-libdir CALIB_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CALIB_1.54.0.zip && rm CALIB_1.54.0.tar.gz CALIB_1.54.0.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 1778k 100 1778k 0 0 7820k 0 --:--:-- --:--:-- --:--:-- 8083k
install for i386
* installing *source* package 'CALIB' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Design.cpp -o Design.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function 'SEXPREC* estimation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NormalizedData.cpp -o NormalizedData.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParameterofOneArray.cpp -o ParameterofOneArray.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RawDataofOneArray.cpp -o RawDataofOneArray.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpikeofOneArray.cpp -o SpikeofOneArray.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CALIB.dll tmp.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.buildbin-libdir/00LOCK-CALIB/00new/CALIB/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CALIB'
finding HTML links ... done
ParameterList-class html
RG html
RGList_CALIB-class html
SpikeList-class html
adjustP2 html
calibReadMe html
cbind html
dim html
dimnames html
estimateParameter html
getColClasses html
merge html
normalizeData html
normdata html
parameter html
plotNormalizedData html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotNormalizedData.Rd:49: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeCI html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeCI.Rd:68: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeCI.Rd:95: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeHI html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeHI.Rd:69: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeHI.Rd:91: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeRG html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeRG.Rd:90: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeSpotError html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeSpotError.Rd:55: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
read.rg html
read.spike html
spike html
subsetting html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CALIB' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Design.cpp -o Design.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function 'SEXPREC* estimation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NormalizedData.cpp -o NormalizedData.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParameterofOneArray.cpp -o ParameterofOneArray.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RawDataofOneArray.cpp -o RawDataofOneArray.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpikeofOneArray.cpp -o SpikeofOneArray.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CALIB.dll tmp.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.buildbin-libdir/CALIB/libs/x64
** testing if installed package can be loaded
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
* MD5 sums
packaged installation of 'CALIB' as CALIB_1.54.0.zip
* DONE (CALIB)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CALIB' successfully unpacked and MD5 sums checked
|
CALIB.Rcheck/examples_i386/CALIB-Ex.timings
|
CALIB.Rcheck/examples_x64/CALIB-Ex.timings
|