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CHECK report for CALIB on merida2

This page was generated on 2018-10-17 08:47:17 -0400 (Wed, 17 Oct 2018).

Package 180/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CALIB 1.46.0
Hui Zhao
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CALIB
Branch: RELEASE_3_7
Last Commit: 9e4bdb0
Last Changed Date: 2018-04-30 10:35:06 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CALIB
Version: 1.46.0
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_1.46.0.tar.gz
StartedAt: 2018-10-16 20:13:40 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:14:21 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 41.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CALIB.Rcheck
Warnings: 1

Command output

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### 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_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CALIB.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.46.0’
* 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:226:30: warning: 'readinparlist' has C-linkage specified, but returns incomplete type 'vector<ParameterofOneArray>' which could be incompatible with C [-Wreturn-type-c-linkage]
See ‘/Users/biocbuild/bbs-3.7-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 ... OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/CALIB.Rcheck/00check.log’
for details.



Installation output

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/3.5/Resources/library’
* installing *source* package ‘CALIB’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Design.cpp -o Design.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Estimation.cpp -o Estimation.o
Estimation.cpp:147:19: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                         ^
Estimation.cpp:147:25: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                               ^
Estimation.cpp:147:30: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                    ^
Estimation.cpp:147:35: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                         ^
Estimation.cpp:147:40: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                              ^
Estimation.cpp:147:49: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                       ^
Estimation.cpp:147:58: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
        char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                                ^
Estimation.cpp:147:67: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-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++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c NormalizedData.cpp -o NormalizedData.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c RawDataofOneArray.cpp -o RawDataofOneArray.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c SpikeofOneArray.cpp -o SpikeofOneArray.o
clang++ -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/3.5/Resources/library/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
* DONE (CALIB)

Tests output


Example timings

CALIB.Rcheck/CALIB-Ex.timings

nameusersystemelapsed
RG0.1440.0120.157
adjustP20.2200.0150.240
calibReadMe0.0010.0000.002
cbind0.0050.0000.004
dim0.0070.0000.008
dimnames0.0060.0010.006
estimateParameter2.2610.0202.296
getColClasses0.0020.0000.002
merge0.0060.0000.007
normalizeData0.3350.0120.351
normdata0.0820.0120.094
parameter0.0470.0020.050
plotNormalizedData0.1250.0110.137
plotSpikeCI0.1610.0130.181
plotSpikeHI0.1090.0070.119
plotSpikeRG0.2410.0160.261
plotSpikeSpotError0.1430.0110.163
read.rg0.0010.0000.001
spike0.0390.0040.044
subsetting0.0040.0000.004