| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-01-16 13:30:43 -0500 (Thu, 16 Jan 2020).
| Package 214/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Hui Zhao
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: CALIB |
| Version: 1.53.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CALIB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CALIB_1.53.1.tar.gz |
| StartedAt: 2020-01-16 02:27:53 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:28:57 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 64.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CALIB.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CALIB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CALIB_1.53.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CALIB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CALIB’ version ‘1.53.1’
* 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 ‘CALIB’ can be installed ... WARNING
Found the following significant warnings:
Estimation.cpp:147:19: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:35: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:40: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:49: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:58: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:147:67: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
Estimation.cpp:226:30: warning: 'readinparlist' has C-linkage specified, but returns incomplete type 'vector<ParameterofOneArray>' which could be incompatible with C [-Wreturn-type-c-linkage]
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
See ‘/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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.Rcheck/00check.log’
for details.
CALIB.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CALIB
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CALIB’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Design.cpp -o Design.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Estimation.cpp -o Estimation.o
Estimation.cpp:147:19: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:30: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:35: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:40: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:49: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:58: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:67: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:226:30: warning: 'readinparlist' has C-linkage specified, but returns incomplete type 'vector<ParameterofOneArray>' which could be incompatible with C [-Wreturn-type-c-linkage]
vector <ParameterofOneArray> readinparlist(SEXP parlist, int ncol)
^
9 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c NormalizedData.cpp -o NormalizedData.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o
In file included from ParameterofOneArray.cpp:4:
./ParameterofOneArray.h:11:9: warning: private field 'SpotErrorofOneSpot' is not used [-Wunused-private-field]
double SpotErrorofOneSpot;
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CALIB/00new/CALIB/libs
** R
** data
** 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
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
** checking absolute paths in shared objects and dynamic libraries
** 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
* DONE (CALIB)
CALIB.Rcheck/CALIB-Ex.timings
| name | user | system | elapsed | |
| RG | 0.174 | 0.025 | 0.199 | |
| adjustP2 | 0.240 | 0.025 | 0.266 | |
| calibReadMe | 0.001 | 0.000 | 0.001 | |
| cbind | 0.008 | 0.002 | 0.009 | |
| dim | 0.017 | 0.004 | 0.021 | |
| dimnames | 0.002 | 0.000 | 0.003 | |
| estimateParameter | 1.906 | 0.038 | 1.945 | |
| getColClasses | 0.001 | 0.001 | 0.002 | |
| merge | 0.013 | 0.001 | 0.014 | |
| normalizeData | 0.332 | 0.022 | 0.354 | |
| normdata | 0.092 | 0.018 | 0.109 | |
| parameter | 0.062 | 0.007 | 0.069 | |
| plotNormalizedData | 0.198 | 0.021 | 0.224 | |
| plotSpikeCI | 0.182 | 0.024 | 0.207 | |
| plotSpikeHI | 0.086 | 0.012 | 0.098 | |
| plotSpikeRG | 0.268 | 0.040 | 0.308 | |
| plotSpikeSpotError | 0.121 | 0.016 | 0.140 | |
| read.rg | 0.000 | 0.000 | 0.001 | |
| spike | 0.066 | 0.010 | 0.077 | |