pdftk: not found

[kevpfowler]

My understanding from the README is that if I have JAVA installed (JDK and JRE), then staplr contains pdftk-java and I do not need to separately install pdftk.

But, when I run the README example, I get "sh: 1: pdftk: not found":

> pdfFile = system.file('testForm.pdf',package = 'staplr')
> pdfFile
[1] "/home/kfowler/R/x86_64-pc-linux-gnu-library/3.6/staplr/testForm.pdf"
> get_fields(pdfFile)
sh: 1: pdftk: not found
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(system_command) : error in running command
2: In file(con, "r") :
  cannot open file '/tmp/RtmpZQhoUu/file165a71ea13f0b': No such file or directory

I am using staplr_2.9.0, with R 3.6.3, on a ubuntu 20.04 system. I ran javareconf, and restarted R before attempting the example above.

$ sudo R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version     : 11.0.7
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/lib/jvm/default-java/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lR

JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

[kevpfowler]

I installed pdftk-java separately on my system, and then the staplr::get_fields() command did not generate that error.

However, neither did it work correctly, returning and empty named list (list of length 0)

[oganm]

The readme is accurate for the development version. The CRAN version still requires pdftk installation. Could you try to install it from github and see if it works?

[kevpfowler]

The other thing I tried was to remove pdftk-java, and then installed pdftk itself, which also installed pdftk-java. I re-ran javareconf, and restart R/RStudio. I still got the same result (zero-length list reading fields from testForm.pdf)

I will try the development version and report back

[kevpfowler]

Ok I used the development version and it seems to work correctly. If I had paid full attention to the version qualifier in the README I could have skipped reporting this, since I was using 2.9.0 from CRAN and the README section specifically said it was for 2.11.0. Though I don't understand why 2.9.0 was not working with the externally installed pdftk.

Just an FYI: To install the development version successfully with R3.6.3, I had to first install XML specifying the repo.

install.packages("XML", repos = "http://www.omegahat.net/R")

[oganm]

@pridiltal did you have time to push the updated version to CRAN? the current dev version has been stable and easier to install and debug.

@kevpfowler any idea why you had to specify the repo when installing XML? For me devtools::install_github does the trick with or without XML installed and there doesn't seem to be any issues with CRAN servers, not right now at least

[pridiltal]

This is a great update of the package. Thank you @oganm . Just submitted to CRAN. I'll update you soon.

[kevpfowler]

@oganm I do not know why I had to specify the repo. I'm running on Ubuntu 20.04. Providing more details below.

This is the error I get when installing staplr with devtools::install_github:

> devtools::install_github("pridiltal/staplr")
Downloading GitHub repo pridiltal/staplr@master
Skipping 1 packages not available: XML
✓  checking for file ‘/tmp/RtmpcJMIRT/remotes405f95d4ed366/pridiltal-staplr-b5b9505/DESCRIPTION’ ...
─  preparing ‘staplr’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘staplr_3.0.0.tar.gz’

Installing package into ‘/home/kfowler/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
ERROR: dependency ‘XML’ is not available for package ‘staplr’
* removing ‘/home/kfowler/R/x86_64-pc-linux-gnu-library/3.6/staplr’
Error: Failed to install 'staplr' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpcJMIRT/file405f9442e4176/staplr_3.0.0.tar.gz’ had non-zero exit status

This is the error I get when trying to install XML package the normal way:

> install.packages("XML")
Installing package into ‘/home/kfowler/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘XML’ is not available (for R version 3.6.3)

This is my repos options setting:

> getOption("repos")
                         CRAN 
"https://cloud.r-project.org" 

This is the successful result specifying the omegahat repo:

> install.packages("XML", repos = "http://www.omegahat.net/R")
Installing package into ‘/home/kfowler/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'http://www.omegahat.net/R/src/contrib/XML_3.99-0.tar.gz'
Content type 'application/x-gzip' length 1547930 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
...
...

After which, the staplr devtools::install_github() works fine.

[oganm]

oh sorry i see the reason now. Current CRAN version of XML requires R>4.0.0 which prevents it's installation from install.packages for you. If you're able to update your R the problem should go away.