Hui Zhao
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CALIB |
| Branch: RELEASE_3_9 |
| Last Commit: b958554 |
| Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:46:26 -0400 (Wed, 16 Oct 2019).
| Package 202/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CALIB 1.50.0 Hui Zhao
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: CALIB |
| Version: 1.50.0 |
| 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_1.50.0.tar.gz |
| StartedAt: 2019-10-16 01:05:30 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:06:30 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 59.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CALIB.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running 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_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CALIB.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.50.0’ * 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 ‘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' which could be incompatible with C [-Wreturn-type-c-linkage] See ‘/Users/biocbuild/bbs-3.9-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 ... 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: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/CALIB.Rcheck/00check.log’ for details.
CALIB.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CALIB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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' which could be incompatible with C [-Wreturn-type-c-linkage]
vector 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/3.6/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
** 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 (CALIB)
CALIB.Rcheck/CALIB-Ex.timings
| name | user | system | elapsed | |
| RG | 0.197 | 0.032 | 0.229 | |
| adjustP2 | 0.297 | 0.042 | 0.341 | |
| calibReadMe | 0.001 | 0.001 | 0.002 | |
| cbind | 0.005 | 0.001 | 0.006 | |
| dim | 0.006 | 0.001 | 0.006 | |
| dimnames | 0.002 | 0.000 | 0.003 | |
| estimateParameter | 2.166 | 0.030 | 2.198 | |
| getColClasses | 0.001 | 0.001 | 0.002 | |
| merge | 0.008 | 0.002 | 0.009 | |
| normalizeData | 0.301 | 0.031 | 0.334 | |
| normdata | 0.065 | 0.011 | 0.076 | |
| parameter | 0.044 | 0.007 | 0.050 | |
| plotNormalizedData | 0.119 | 0.018 | 0.140 | |
| plotSpikeCI | 0.193 | 0.029 | 0.226 | |
| plotSpikeHI | 0.133 | 0.013 | 0.147 | |
| plotSpikeRG | 0.329 | 0.041 | 0.372 | |
| plotSpikeSpotError | 0.121 | 0.018 | 0.142 | |
| read.rg | 0 | 0 | 0 | |
| spike | 0.071 | 0.011 | 0.083 | |
| subsetting | 0.005 | 0.001 | 0.006 | |