Question: GenomeInfoDbData not available for Mac
0
gravatar for svetlana.gorokhova
16 months ago by
svetlana.gorokhova0 wrote:

Hi,

I'm trying to install ExomeDepth on MacOS 10.13.5 using R 3.5.1. I installed all the necessary packages without problems exepts for GenomeInfoDbData. It seems not to be available for Mac on bioconductor...
Please help me figure out how to solve this issue.
thanks!

 

Error in install.packages : file ‘~/Downloads/GenomeInfoDbData_1.1.0.tar’ is not a macOS binary package

> install.packages("GenomeInfoDbData")
Installing package into ‘/Users/dgmbc/Library/R/3.5/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘GenomeInfoDbData’ is not available (for R version 3.5.1)

 

ADD COMMENTlink modified 16 months ago • written 16 months ago by svetlana.gorokhova0

It is available. Please cut-and-paste the command that you use and the output.

ADD REPLYlink written 16 months ago by Martin Morgan ♦♦ 24k
Answer: GenomeInfoDbData not available for Mac
0
gravatar for svetlana.gorokhova
16 months ago by
svetlana.gorokhova0 wrote:

> biocLite("GenomeIndoDbData")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘GenomeIndoDbData’
installation path not writeable, unable to update packages: foreign, survival
Old packages: 'ExomeDepth'
Update all/some/none? [a/s/n]: 
a
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘ExomeDepth’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘ExomeDepth’

essai de l'URL 'http://cran.rstudio.com/src/contrib/ExomeDepth_1.1.10.tar.gz'
Content type 'application/x-gzip' length 1679604 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘ExomeDepth’ ...
** package ‘ExomeDepth’ correctement décompressé et sommes MD5 vérifiées
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CNV_estimate.cpp -o CNV_estimate.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_gamma.c -o VP_gamma.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_infnan.c -o VP_infnan.o
VP_infnan.c:127:15: warning: 'gsl_finite' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
    return (! gsl_finite(x)) && (! gsl_isnan(x));
              ^
/usr/include/math.h:757:12: note: 'gsl_finite' has been explicitly marked deprecated here
extern int finite(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
           ^
./config.h:263:16: note: expanded from macro 'finite'
#define finite gsl_finite
               ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_log.c -o VP_log.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_psi.c -o VP_psi.o
VP_psi.c:843:8: warning: 'gsl_finite' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
    if(GSL_IS_REAL(GSL_REAL(cotzpi)) && GSL_IS_REAL(GSL_IMAG(cotzpi)))
       ^
./gsl_math.h:117:25: note: expanded from macro 'GSL_IS_REAL'
#define GSL_IS_REAL(x) (gsl_finite(x))
                        ^
/usr/include/math.h:757:12: note: 'gsl_finite' has been explicitly marked deprecated here
extern int finite(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
           ^
./config.h:263:16: note: expanded from macro 'finite'
#define finite gsl_finite
               ^
VP_psi.c:843:41: warning: 'gsl_finite' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
    if(GSL_IS_REAL(GSL_REAL(cotzpi)) && GSL_IS_REAL(GSL_IMAG(cotzpi)))
                                        ^
./gsl_math.h:117:25: note: expanded from macro 'GSL_IS_REAL'
#define GSL_IS_REAL(x) (gsl_finite(x))
                        ^
/usr/include/math.h:757:12: note: 'gsl_finite' has been explicitly marked deprecated here
extern int finite(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
           ^
./config.h:263:16: note: expanded from macro 'finite'
#define finite gsl_finite
               
 

ADD COMMENTlink written 16 months ago by svetlana.gorokhova0
Answer: GenomeInfoDbData not available for Mac
0
gravatar for svetlana.gorokhova
16 months ago by
svetlana.gorokhova0 wrote:

2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_trig.c -o VP_trig.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_zeta.c -o VP_zeta.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c beta.c -o beta.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c elementary.c -o elementary.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c error.c -o error.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c exp.c -o exp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fdiv.c -o fdiv.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmm.cpp -o hmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hypot.c -o hypot.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c invhyp.c -o invhyp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ldfrexp.c -o ldfrexp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c log1p.c -o log1p.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c math.c -o math.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c stream.c -o stream.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 ExomeDepth.so CNV_estimate.o VP_gamma.o VP_infnan.o VP_log.o VP_psi.o VP_trig.o VP_zeta.o beta.o elementary.o error.o exp.o fdiv.o hmm.o hypot.o invhyp.o ldfrexp.o log1p.o math.o stream.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/dgmbc/Library/R/3.5/library/ExomeDepth/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
ERROR: lazy loading failed for package ‘ExomeDepth’
* removing ‘/Users/dgmbc/Library/R/3.5/library/ExomeDepth’
* restoring previous ‘/Users/dgmbc/Library/R/3.5/library/ExomeDepth’

The downloaded source packages are in
    ‘/private/var/folders/bd/bxqdxgmj70bbj56sjzxcwjn40000gp/T/RtmpQgBuqP/downloaded_packages’
Warning messages:
1: package ‘GenomeIndoDbData’ is not available (for R version 3.5.1) 
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘ExomeDepth’ had non-zero exit status

ADD COMMENTlink written 16 months ago by svetlana.gorokhova0

Simplify things by first trying to install GenomeInfoDbData itself

biocLite("GenomeInfoDbData")

if that's successful, move on to ExomeDepth

ADD REPLYlink written 16 months ago by Martin Morgan ♦♦ 24k
Answer: GenomeInfoDbData not available for Mac
0
gravatar for svetlana.gorokhova
16 months ago by
svetlana.gorokhova0 wrote:

 

installing GenomeInfoDbData worked now, but ExomeDepth still gives error: 

               ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_trig.c -o VP_trig.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VP_zeta.c -o VP_zeta.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c beta.c -o beta.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c elementary.c -o elementary.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c error.c -o error.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c exp.c -o exp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fdiv.c -o fdiv.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmm.cpp -o hmm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hypot.c -o hypot.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c invhyp.c -o invhyp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ldfrexp.c -o ldfrexp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c log1p.c -o log1p.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c math.c -o math.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c stream.c -o stream.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 ExomeDepth.so CNV_estimate.o VP_gamma.o VP_infnan.o VP_log.o VP_psi.o VP_trig.o VP_zeta.o beta.o elementary.o error.o exp.o fdiv.o hmm.o hypot.o invhyp.o ldfrexp.o log1p.o math.o stream.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/dgmbc/Library/R/3.5/library/ExomeDepth/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 (ExomeDepth)

The downloaded source packages are in
    ‘/private/var/folders/bd/bxqdxgmj70bbj56sjzxcwjn40000gp/T/RtmpQgBuqP/downloaded_packages’
installation path not writeable, unable to update packages: foreign, survival

ADD COMMENTlink modified 16 months ago • written 16 months ago by svetlana.gorokhova0
Answer: GenomeInfoDbData not available for Mac
0
gravatar for svetlana.gorokhova
16 months ago by
svetlana.gorokhova0 wrote:

__________________

ADD COMMENTlink modified 16 months ago • written 16 months ago by svetlana.gorokhova0
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