Error on Install in PatientLevelPrediction

[ericaVoss]

I want to use the patient level prediction package. Followed the README and ran the following:

install.packages("devtools")
library(devtools)
install_github("ohdsi/SqlRender") 
install_github("ohdsi/DatabaseConnector") 
install_github("ohdsi/Cyclops") 
install_github("ohdsi/PatientLevelPrediction") 

I'm getting the following error on the last install:

install_github("ohdsi/PatientLevelPrediction")
Downloading github repo ohdsi/PatientLevelPrediction@master
Installing PatientLevelPrediction
Skipping 3 packages not available: Cyclops, DatabaseConnector, SqlRender
Installing 1 packages: plyr
package ‘plyr’ successfully unpacked and MD5 sums checked
"C:/PROGRA~1/R/R-31~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/evoss3/AppData/Local/Temp/RtmpUjd8iL/devtoolsc68320a72e7/OHDSI-PatientLevelPrediction-72f9445"  \
  --library="C:/Users/evoss3/Documents/R/win-library/3.1" --install-tests 

* installing *source* package 'PatientLevelPrediction' ...
** libs

*** arch - i386
make: Nothing to be done for `all'.
installing to C:/Users/evoss3/Documents/R/win-library/3.1/PatientLevelPrediction/libs/i386

*** arch - x64
make: Nothing to be done for `all'.
installing to C:/Users/evoss3/Documents/R/win-library/3.1/PatientLevelPrediction/libs/x64
** R
** inst
** preparing package for lazy loading
Warning: package 'RJDBC' was built under R version 3.1.2
Warning: package 'DBI' was built under R version 3.1.3
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Warning: package 'RJDBC' was built under R version 3.1.2
Warning: package 'DBI' was built under R version 3.1.3
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'C:/Users/evoss3/Documents/R/win-library/3.1/PatientLevelPrediction/libs/i386/PatientLevelPrediction.dll':
  LoadLibrary failure:  %1 is not a valid Win32 application.

Error: loading failed
Execution halted
*** arch - x64
Warning: package 'RJDBC' was built under R version 3.1.2
Warning: package 'DBI' was built under R version 3.1.3
ERROR: loading failed for 'i386'
* removing 'C:/Users/evoss3/Documents/R/win-library/3.1/PatientLevelPrediction'
Error: Command failed (1)

Am I missing a pre-req?

[schuemie]

Sorry about that! There were some files in the repo that shouldn't have been there. Can you try again?

[ericaVoss]

So I reran this:

install.packages("devtools")
library(devtools)
install_github("ohdsi/SqlRender") 
install_github("ohdsi/DatabaseConnector") 
install_github("ohdsi/Cyclops") 
install_github("ohdsi/PatientLevelPrediction") 

I'm now getting failures with Cyclops.

> install_github("ohdsi/Cyclops") 
Downloading github repo ohdsi/Cyclops@master
Installing Cyclops
Installing 4 packages: BH, Rcpp, RcppEigen, RcppParallel
package ‘BH’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘BH’
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
package ‘RcppEigen’ successfully unpacked and MD5 sums checked
package ‘RcppParallel’ successfully unpacked and MD5 sums checked
"C:/PROGRA~1/R/R-31~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/evoss3/AppData/Local/Temp/RtmpiiBJ4v/devtools76c50d72804/OHDSI-Cyclops-57327d5" --library="C:/Program  \
  Files/R/R-3.1.1/library" --install-tests 

ERROR: dependencies 'Rcpp', 'BH' are not available for package 'Cyclops'
* removing 'C:/Program Files/R/R-3.1.1/library/Cyclops'
Error: Command failed (1)
> install_github("ohdsi/PatientLevelPrediction")
Downloading github repo ohdsi/PatientLevelPrediction@master
Installing PatientLevelPrediction
Skipping 3 packages not available: Cyclops, DatabaseConnector, SqlRender
Installing 11 packages: colorspace, digest, ggplot2, labeling, magrittr, plyr, RColorBrewer, Rcpp, reshape2, stringi, stringr
package ‘colorspace’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘digest’
package ‘ggplot2’ successfully unpacked and MD5 sums checked
package ‘labeling’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘plyr’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘plyr’
package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
package ‘reshape2’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘stringr’ successfully unpacked and MD5 sums checked
"C:/PROGRA~1/R/R-31~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/evoss3/AppData/Local/Temp/RtmpiiBJ4v/devtools76c1849b4d/OHDSI-PatientLevelPrediction-f9cc776" --library="C:/Program  \
  Files/R/R-3.1.1/library" --install-tests 

ERROR: dependencies 'Cyclops', 'plyr', 'Rcpp' are not available for package 'PatientLevelPrediction'
* removing 'C:/Program Files/R/R-3.1.1/library/PatientLevelPrediction'
Error: Command failed (1)

[msuchard]

This does not look like an error with Cyclops. There's probably something strange about your installs of the R packages BH and Rcpp. I'd suggest manually updating these via:

install.packages("BH")
install.packages("Rcpp")

[ericaVoss]

I think that worked, thank you @schuemie & @msuchard!