rsconnect says package is sourced from CRAN but I installed from GitHub....leads to failure of Shiny app to deploy correctly.

[Kevin Little]

Hi, I have an app previously uploaded to shinyapps.io server and functional two months ago.   I have worked locally on related project in the last few weeks and appear to have loaded the openxlsx package from GitHub since the last app deployment 

I used devtools, version 1.10.0 to install openxlsx

On attempt to redeploy the app today, I seem to have confused things.  Hoping for suggestions to get the Shiny app loaded successfully without reverting back to the CRAN version of openxlsx and to understand what happened here!.

Thanks

DETAILS

rsconnect::appDependencies shows that the openxlsx package is from CRAN??      

rsconnect::appDependencies()

        package  version source

1            BH 1.60.0-1   CRAN

2           DBI    0.3.1   CRAN

3           PKI    0.1-3   CRAN

4            R6    2.1.2   CRAN

5         RCurl 1.95-4.8   CRAN

6       RJSONIO    1.3-0   CRAN

7          Rcpp   0.12.4   CRAN

8       Rmonkey    0.3.1   CRAN

9           XML 3.98-1.4   CRAN

10   assertthat      0.1   CRAN

11    base64enc    0.1-3   CRAN

12       bitops    1.0-6   CRAN

13   cellranger    1.0.0   CRAN

14         curl    0.9.6   CRAN

15     devtools   1.10.0   CRAN

16       digest    0.6.9   CRAN

17        dplyr    0.4.3   CRAN

18        git2r   0.13.1   CRAN

19 googlesheets    0.2.0   CRAN

20    htmltools      0.3   CRAN

21       httpuv    1.3.3   CRAN

22         httr    1.1.0   CRAN

23     jsonlite   0.9.19   CRAN

24     lazyeval   0.1.10   CRAN

25     magrittr      1.5   CRAN

26      memoise    1.0.0   CRAN

27         mime      0.4   CRAN

28       miniUI    0.1.1   CRAN

29      openssl    0.9.2   CRAN

30     openxlsx    3.1.9   CRAN

31      packrat  0.4.7-1   CRAN

32         plyr    1.8.3   CRAN

33        purrr    0.2.1   CRAN

34        readr    0.2.2   CRAN

35     reshape2    1.4.1   CRAN

36    rsconnect  0.4.2.1   CRAN

37   rstudioapi      0.5   CRAN

38        shiny   0.13.2   CRAN

39    shinyapps   0.3.63 github

40      shinyjs    0.5.2   CRAN

41      stringi    1.0-1   CRAN

42      stringr    1.0.0   CRAN

43        tidyr    0.4.1   CRAN

44      whisker    0.3-2   CRAN

45        withr    1.0.1   CRAN

46         xml2    0.1.2   CRAN

47       xtable    1.8-2   CRAN

48         yaml   2.1.13   CRAN

But the CRAN version is clearly 3.0.0 not 3.1.9.  

Error occurs on building the app on shinyio server, as the build routine can't find openxlsx 3.1.9 on CRAN (which is correct, the CRAN version is 3.0.0, https://cran.r-project.org/ )   

sessionInfo()

R version 3.2.3 (2015-12-10)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          

[5] LC_TIME=English_United States.1252    

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):

 [1] httr_1.1.0        R6_2.1.2          rsconnect_0.4.2.1 tools_3.2.3      

 [5] withr_1.0.1       curl_0.9.6        memoise_1.0.0     knitr_1.12.3     

 [9] git2r_0.13.1      digest_0.6.9      packrat_0.4.7-1   devtools_1.10.0  

[Tareef Kawaf]

I wonder if there is a bug in the rsconnect package.

I am guessing here, but I would try the following, one step at a time and see if they make a difference:

1. Update to the latest version of rsconnect:  devtools::install_github("rstudio/rsconnect"), and try again.

2. Uninstall the openxlsx package and re-install it, and try again.

3. Upgrade devtools , and repeat steps #1 and #2.

--
You received this message because you are subscribed to the Google Groups "ShinyApps Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to shinyapps-use...@googlegroups.com.
To post to this group, send email to shinyap...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/fe0e1834-ddbf-40f8-9719-cb95bb9620cf%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Kevin Little]

Thanks, did not fix.   rsconnect still has openxlsx as sourced on CRAN.    Here are the details:

1.      After step 1, rsconnect::appDependencies() still shows source for openxlsx as CRAN.

 

 

2.      After step 2, on reinstall of openxlsx from GitHub, I get:

 

Warning message:

In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :

  there is no package called ‘openxlsx’

 

However the directory exists in my library

(I did note that using remove.packages(“openxlsx”) did not remove everything—there was openxlsx.dll file still in the libs folder).

 

This may be related to the information seen on loading:

 

> devtools::install_github("awalker89/openxlsx")

Downloading GitHub repo awalker89/openxlsx@master

from URL https://api.github.com/repos/awalker89/openxlsx/zipball/master

Installing openxlsx

"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \

  "C:/Users/Kevin/AppData/Local/Temp/RtmpMRWH8P/devtools36a85c647e70/awalker89-openxlsx-7ecbcfa"  \

  --library="C:/Users/Kevin/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'openxlsx' ...

** libs

g++ -m64 -I"C:/PROGRA~1/R/R-32~1.3/include" -DNDEBUG    -I"C:/Users/Kevin/Documents/R/win-library/3.2/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o

g++ -m64 -I"C:/PROGRA~1/R/R-32~1.3/include" -DNDEBUG    -I"C:/Users/Kevin/Documents/R/win-library/3.2/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cppFunctions.cpp -o cppFunctions.o

cppFunctions.cpp: In function 'SEXPREC* loadworksheets(Rcpp::Reference, Rcpp::List, std::vector<std::basic_string<char> >, Rcpp::LogicalVector)':

cppFunctions.cpp:3335:41: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]

g++ -m64 -shared -s -static-libgcc -o openxlsx.dll tmp.def RcppExports.o cppFunctions.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LC:/PROGRA~1/R/R-32~1.3/bin/x64 -lR

installing to C:/Users/Kevin/Documents/R/win-library/3.2/openxlsx/libs/x64

** R

** inst

** tests

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (openxlsx)

 

In any case, the openxlsx package is still listed by appDependencies as sourced on CRAN.

36    rsconnect  0.4.2.2 github

37   rstudioapi      0.5   CRAN

38        shiny   0.13.2   CRAN

39    shinyapps   0.3.63 github

40      shinyjs    0.5.2   CRAN

41      stringi    1.0-1   CRAN

42      stringr    1.0.0   CRAN

43        tidyr    0.4.1   CRAN

44      whisker    0.3-2   CRAN

45        withr    1.0.1   CRAN

46         xml2    0.1.2   CRAN

47       xtable    1.8-2   CRAN

48         yaml   2.1.13   CRAN

 

Step 3.    Trying to install devtools, also the system cannot automatically remove the devtools.dll in folder devtools/libs/x64   Removed the .dll file manually.  Reran the install.packages for devtools.

 

> devtools::install_github("rstudio/rsconnect")

Downloading GitHub repo rstudio/rsconnect@master

from URL https://api.github.com/repos/rstudio/rsconnect/zipball/master

Installing rsconnect

"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \

  "C:/Users/Kevin/AppData/Local/Temp/RtmpgX36tV/devtools3cc064525c0d/rstudio-rsconnect-aac8077"  \

  --library="C:/Users/Kevin/Documents/R/win-library/3.2" --install-tests 

ERROR: failed to lock directory 'C:/Users/Kevin/Documents/R/win-library/3.2' for modifying

Try removing 'C:/Users/Kevin/Documents/R/win-library/3.2/00LOCK-rstudio-rsconnect-aac8077'

Error: Command failed (3)

 

Removed the file as suggested.   Reran the install command.  Successfully installed.

Had to manually remove the openxlsx.dll from libs/x64 folder.

 

Same messages on installing openxlsx:

> devtools::install_github("awalker89/openxlsx")

Downloading GitHub repo awalker89/openxlsx@master

from URL https://api.github.com/repos/awalker89/openxlsx/zipball/master

Installing openxlsx

"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \

  "C:/Users/Kevin/AppData/Local/Temp/Rtmp8AVkxH/devtools444477e5bc4/awalker89-openxlsx-7ecbcfa"  \

  --library="C:/Users/Kevin/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'openxlsx' ...

** libs

g++ -m64 -I"C:/PROGRA~1/R/R-32~1.3/include" -DNDEBUG    -I"C:/Users/Kevin/Documents/R/win-library/3.2/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o

g++ -m64 -I"C:/PROGRA~1/R/R-32~1.3/include" -DNDEBUG    -I"C:/Users/Kevin/Documents/R/win-library/3.2/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cppFunctions.cpp -o cppFunctions.o

cppFunctions.cpp: In function 'SEXPREC* loadworksheets(Rcpp::Reference, Rcpp::List, std::vector<std::basic_string<char> >, Rcpp::LogicalVector)':

cppFunctions.cpp:3335:41: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]

g++ -m64 -shared -s -static-libgcc -o openxlsx.dll tmp.def RcppExports.o cppFunctions.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LC:/PROGRA~1/R/R-32~1.3/bin/x64 -lR

installing to C:/Users/Kevin/Documents/R/win-library/3.2/openxlsx/libs/x64

** R

** inst

** tests

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (openxlsx)

Warning message:

In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :

  there is no package called ‘openxlsx’

 

on running rsconnect::appDependencies(), shows that openxlsx was sourced from CRAN and is version 3.1.9.   

For now, I am going to use the CRAN version of openxlsx and also post an issue to awalker's github account for openxlsx, just in case there is something in the package build.

[Kevin Little]

rsconnect still believes that openxlsx was sourced from CRAN.