Error on latest install of KeppraAngioedema

[jduke99]

I am getting this for a few of the packages (on Windows):

Warning in install.packages : cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found' Warning in install.packages : cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found' Warning in install.packages : unable to access index for repository http://OHDSI.github.io/drat/bin/windows/contrib/3.2: cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES' Warning in install.packages : cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found' Warning in install.packages : cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found' Warning in install.packages : unable to access index for repository http://cloudyr.github.io/drat/bin/windows/contrib/3.2: cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES'

[msuchard]

@jduke99, this is likely not an error, just a warning that drat repos do not contain precompiled R package versions. What do you see after

library(KeppraAngioedema)

?

[jduke99]

It does not install KeppraAngioedema library due to s3 and OhdsiSharing issue (at bottom):

> install.packages("KeppraAngioedema")
also installing the dependencies ‘aws.signature’, ‘uuid’, ‘base64enc’, ‘aws.s3’, ‘DatabaseConnector’, ‘FeatureExtraction’, ‘CohortMethod’, ‘EmpiricalCalibration’, ‘OhdsiSharing’

Warning: unable to access index for repository http://OHDSI.github.io/drat/bin/macosx/mavericks/contrib/3.2
Warning: unable to access index for repository http://cloudyr.github.io/drat/bin/macosx/mavericks/contrib/3.2

  There are binary versions available but the source versions are later:
                     binary source needs_compilation
aws.signature         0.2.0  0.2.1             FALSE
EmpiricalCalibration  1.1.0  1.1.1             FALSE

Packages which are only available in source form, and may need compilation of
  C/C++/Fortran: ‘FeatureExtraction’ ‘CohortMethod’
Do you want to attempt to install these from sources?
y/n: y

trying URL 'https://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.2/uuid_0.1-2.tgz'
Content type 'application/x-gzip' length 24678 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'https://cran.fhcrc.org/bin/macosx/mavericks/contrib/3.2/base64enc_0.1-3.tgz'
Content type 'application/x-gzip' length 26679 bytes (26 KB)
==================================================
downloaded 26 KB

The downloaded binary packages are in
    /var/folders/yl/m9jq1dz17dj6jwld6rfsq8m80000gn/T//RtmpLV2qPg/downloaded_packages
installing the source packages ‘aws.signature’, ‘aws.s3’, ‘DatabaseConnector’, ‘FeatureExtraction’, ‘CohortMethod’, ‘EmpiricalCalibration’, ‘OhdsiSharing’, ‘KeppraAngioedema’

trying URL 'http://cloudyr.github.io/drat/src/contrib/aws.signature_0.2.1.tar.gz'
Content type 'application/octet-stream' length 7168 bytes
==================================================
downloaded 7168 bytes

trying URL 'http://cloudyr.github.io/drat/src/contrib/aws.s3_0.1.26.tar.gz'
Content type 'application/octet-stream' length 25252 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'http://OHDSI.github.io/drat/src/contrib/DatabaseConnector_1.4.0.tar.gz'
Content type 'application/octet-stream' length 6813244 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

trying URL 'http://OHDSI.github.io/drat/src/contrib/FeatureExtraction_1.0.0.tar.gz'
Content type 'application/octet-stream' length 457542 bytes (446 KB)
==================================================
downloaded 446 KB

trying URL 'http://OHDSI.github.io/drat/src/contrib/CohortMethod_2.0.2.tar.gz'
Content type 'application/octet-stream' length 1904312 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'http://OHDSI.github.io/drat/src/contrib/EmpiricalCalibration_1.1.1.tar.gz'
Content type 'application/octet-stream' length 317309 bytes (309 KB)
==================================================
downloaded 309 KB

trying URL 'http://OHDSI.github.io/drat/src/contrib/OhdsiSharing_0.1.1.tar.gz'
Content type 'application/octet-stream' length 12599 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'http://OHDSI.github.io/drat/src/contrib/KeppraAngioedema_0.1.0.tar.gz'
Content type 'application/octet-stream' length 106204 bytes (103 KB)
==================================================
downloaded 103 KB

* installing *source* package ‘aws.signature’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aws.signature)
* installing *source* package ‘DatabaseConnector’ ...
** R
** inst
** preparing package for lazy loading
Warning: package ‘rJava’ was built under R version 3.2.3
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: package ‘rJava’ was built under R version 3.2.3
* DONE (DatabaseConnector)
* installing *source* package ‘EmpiricalCalibration’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EmpiricalCalibration)
* installing *source* package ‘aws.s3’ ...
** R
** inst
** preparing package for lazy loading
Error : object ‘http_error’ is not exported by 'namespace:httr'
ERROR: lazy loading failed for package ‘aws.s3’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/aws.s3’
* installing *source* package ‘FeatureExtraction’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c ByMax.cpp -o ByMax.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c BySum.cpp -o BySum.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppWrapper.cpp -o RcppWrapper.o
clang++ -std=c++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 FeatureExtraction.so ByMax.o BySum.o RcppExports.o RcppWrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/FeatureExtraction/libs
** R
** inst
** preparing package for lazy loading
Warning: package ‘rJava’ was built under R version 3.2.3
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package ‘rJava’ was built under R version 3.2.3
* DONE (FeatureExtraction)
* installing *source* package ‘CohortMethod’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c Auc.cpp -o Auc.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c BySum.cpp -o BySum.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c Match.cpp -o Match.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppWrapper.cpp -o RcppWrapper.o
clang++ -std=c++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 CohortMethod.so Auc.o BySum.o Match.o RcppExports.o RcppWrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/CohortMethod/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: package ‘rJava’ was built under R version 3.2.3
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘MultipleAnalyses.Rmd’ using ‘UTF-8’ 
   ‘SingleStudies.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded
Warning: package ‘rJava’ was built under R version 3.2.3
* DONE (CohortMethod)
ERROR: dependency ‘aws.s3’ is not available for package ‘OhdsiSharing’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/OhdsiSharing’
ERROR: dependency ‘OhdsiSharing’ is not available for package ‘KeppraAngioedema’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/KeppraAngioedema’

The downloaded source packages are in
    ‘/private/var/folders/yl/m9jq1dz17dj6jwld6rfsq8m80000gn/T/RtmpLV2qPg/downloaded_packages’
Warning messages:
1: In install.packages("KeppraAngioedema") :
  installation of package ‘aws.s3’ had non-zero exit status
2: In install.packages("KeppraAngioedema") :
  installation of package ‘OhdsiSharing’ had non-zero exit status
3: In install.packages("KeppraAngioedema") :
  installation of package ‘KeppraAngioedema’ had non-zero exit status

[jduke99]

I see the core error. Let me try to install s3 manually and reload package

Error : object ‘http_error’ is not exported by 'namespace:httr' ERROR: lazy loading failed for package ‘aws.s3’

• removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/aws.s3’

[msuchard]

Actually, the error appears to be an old version of httr on your system (imported by aws.s3. Unfortunately, we have no control over the explicit dependencies in aws.s3 since it's not our package. But, I can add a dependency on a newer version of httr in OhdsiSharing. Working on this. Don't manually update, because I want our install to work on all system.

[jduke99]

Got it. Thanks.

[msuchard]

OK. In about 10 minutes (after CI pipes the new OhdsiSharing to our drat repo), try:

install.packages("KeppraAngioedema")

again. If it fails, then post what gets reported by library(help=httr)

[jduke99]

Success!!

library(KeppraAngioedema) Loading required package: DatabaseConnector Loading required package: RJDBC Loading required package: DBI Loading required package: rJava