html reports are NOT being generated - Dependencies not fulfilled

[rafinhacp]

Hello all!

I'm trying to run FastqPuri on my MacBook (OS Catalina 10.15.5) and I'm getting the following warning/error when running the test provided:

Qreport from FastqPuri -Input file: ../test.fq.bz2 -Read length: 51 -Number of tiles: 96 -Min quality: 27 -Qualities for properties plot: 27,33,37 -Output bin-file : my_test_output.bin -Output html-file : my_test_output.html -Output info-file: my_test_output.info Starting Qreport at: Mon Jul 20 15:26:52 2020 -Reading a filtered file? no. -Finished reading file. WARNING: expected 96 tiles but found only 20. -Writing data structure to file my_test_output.bin. WARNING: html reports are NOT being generated. Dependencies not fulfilled. Finishing program at: Mon Jul 20 15:26:55 2020 Time elapsed: 0.791192 s.

However, I've checked and:

• my cmake is version 3.17.3;
• I have pandoc installed, version 2.10 (installed through home-brew, following the instruction here https://pandoc.org/installing.html)
• I have R installed (version 3.6.3) and all required R packages installed (pheatmap, knitr, rmarkdown).

I also tried to run FastqPuri in my lab's server (OS Ubuntu 14) and I get the same warning/error: WARNING: html reports are NOT being generated. Dependencies not fulfilled.

In the server:

• cmake version 3.2.2 is installed;
• pandoc 1.19.2.1 is installed;
• R version 3.3.0 is installed and required packages are also installed (pheatmap, knitr, rmarkdown)

So, the Qreport generates the my_test_output.bin and the my_test_output.info but not the html file.

If I try to run Sreport, it gives me the following: Sreport from FastqPuri -Input folder: ./ -Rmd-file used to generate HTML: /usr/local/share/FastqPuri/R/summary_report.Rmd -Output file: my_test_summary_report.html Starting Sreport at: Mon Jul 20 13:44:09 2020 WARNING: html reports are NOT being generated. Dependencies not fulfilled. Finishing program at: Mon Jul 20 13:44:09 2020 Time elapsed: 0.000271 s.

The thing is: I can't know which dependencies are missing because the warning only tells me something is missing. Everything said to be a dependency or a requirement for FastqPuri to work is installed.

Does anyone knows what could me missing to be causing html files not to be generated? If anyone has gone through this problem and can help me, I'll be very grateful.

Thanks in advance.

[PaulaAlessio]

Hi,

Do you have an updated repository? If so, when you type the command:

cmake -H. -Bbuild

You should be able to see whether your dependencies are fulfilled. The expected output is:

-- Check for pandoc: /usr/bin/pandoc
-- Check for Rscript: /usr/bin/Rscript
-- Check for gunzip: /usr/bin/gunzip
-- Check for gzip: /usr/bin/gzip
-- Found R_rmarkdown: TRUE  
-- Found R_pheatmap: TRUE  
-- Found R_knitr: TRUE  

[rafinhacp]

Hi Paula!

When I try this command you suggested, I have the following output: cmake: /usr/local/lib/libcurl.so.4: no version information available (required by cmake) -- Check the prefix for root installation: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri -- uint8_t size: 1 bytes -- uint16_t size: 2 bytes -- uint32_t size: 4 bytes -- uint64_t size: 8 bytes -- Check for pandoc: /home/raperez/sw/ANACONDA_v5.0.1/installation_dir/bin/pandoc -- Check for Rscript: /usr/local/bin/Rscript -- Check for gunzip: /bin/gunzip -- Check for gzip: /bin/gzip -- Setting Illumina maximum read length: READ_MAXLEN 400 -- Setting Rmd quality report file: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/quality_report.Rmd -- Setting Rmd summary report file: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/summary_report.Rmd -- Setting Rmd summary filter report file: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/summary_filter_report.Rmd -- Setting Rmd summary filter report file for DS data: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/summary_filter_reportDS.Rmd -- Setting compiler flags: -Wall -Wextra -O3 -march=native -std=c11 -D_DEFAULT_SOURCE -- Configuring done -- Generating done -- Build files have been written to: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/build

I understand the repository is updated, but he libraries pheatmap, knitr and rmarkdown are not found. I double-checked and they are installed in the default path of R. I tried to install then locally and define the path using 'R_LIBS', but it did not work, the libraries are not being found.

Could be that the R version I'm using (version 3.3.0) is not adequate? Is it necessary to have a specific version of R? Does FastqPuri uses the default path to look for the R libraries?

[PaulaAlessio]

Hi,

can you check the following:

• make sure you have Rscript, and if so check its location (mine is /usr/bin/Rscript)
• if you do not have it install it.
• Run:

  Rscript --slave -e "library('pheatmap')"
  Rscript --slave -e "library('knitr')"
  Rscript --slave -e "library('rmarkdown')"

  if one of them is not recognized, it will tell you something like

  Error in library("knitr") : there is no package called 'knitr'
  Execution halted

• If none of them "complains", this is, there is no output, then, proceed as follows:
  • Remove the folder build
  • Repo update (just in case): git pull
  • Compile again: cmake -H. -Bbuild

[rafinhacp]

Hi Paula,

Yes, I have Rscript, the location is /usr/local/bin/Rscript

When I ran Rscript --slave -e "library('pheatmap')" Rscript --slave -e "library('knitr')" Rscript --slave -e "library('rmarkdown')"

I got the same warning message for all of them, so no "complains": During startup - Warning message: Setting LC_CTYPE failed, using "C"

I then proceeded as you suggested and again, the output for cmake -H. -Bbuild was the same as before: it can't "see" the R libraries. And the output to git pull is Already up-to-date.

I don't have sudo access in the machine and I'm still learningh programming. I think there is a problem with R versions in the server (that maybe were not completely uninstall or there are different versions installed locally and globally). Do you have any suggestion of modification I could do in the file CMakeLists.txt so during the build of FastqPuri a version of R is specified?

I'm open to any other suggestions as well. Thanks in advance.

[PaulaAlessio]

Hi, The problem is the warning message, I am afraid. You can either,

• Try to remove the warning message, by doing this (I do not know whether it will work, but you can give it a try, or try to google it)
  • Open a terminal
  • Write or paste in: defaults write org.R-project.R force.LANG en_US.UTF-8
• Modify the file Cmakelists.txt by commenting the lines (adding the # symbol):

  set(HAVE_RPKG FALSE)
  if(RSCRIPT_EXEC AND HAVE_PANDOC)
  find_r_package(rmarkdown ${RSCRIPT_EXEC})
  find_r_package(pheatmap ${RSCRIPT_EXEC})
  find_r_package(knitr ${RSCRIPT_EXEC})
  if (R_rmarkdown AND R_pheatmap AND R_knitr)
    set(HAVE_RPKG TRUE)
  endif(R_rmarkdown AND R_pheatmap AND R_knitr)
  endif(RSCRIPT_EXEC AND HAVE_PANDOC)

  And simply adding the line

  set(HAVE_RPKG TRUE)

Then, try to generate the reports again...

If that does not work either, we can set the variable HAVE_RPKG to true by hand, but let's true this first.

[rafinhacp]

Hi,

I tried modifying the Cmakelists.txt file as you specified in your previous message, but reports are still not generated:

Qreport from FastqPuri

• Input file: ../test.fq.bz2
• Read length: 51
• Number of tiles: 96
• Min quality: 27
• Qualities for properties plot: 27,33,37
• Output bin-file : my_test_output.bin
• Output html-file : my_test_output.html
• Output info-file: my_test_output.info Starting Qreport at: Wed Aug 19 13:02:07 2020
• Reading a filtered file? no.
• Finished reading file. WARNING: expected 96 tiles but found only 20.
• Writing data structure to file my_test_output.bin. WARNING: html reports are NOT being generated. Dependencies not fulfilled. Finishing program at: Wed Aug 19 13:02:11 2020 Time elapsed: 1.208423 s.

Should we set the variable HAVE_RPKG by hand?

[PaulaAlessio]

Uhm... Weird. Have you removed the build directory and run cmake again ?

No entiendo que no funcione. Si no, sí, haz un grep a la cadena HAVE_RPKG, abre el fichero y dale el valor correcto.

[rafinhacp]

Hi Paula,

yes, I changed the Cmakelists.txt, deleted the build directory, ran $ cmake -H. -Bbuild/ [-DRSCRIPT=/path/to/my/R/bin/Rscript] [-DCMAKE_INSTALL_PREFIX=/path/to/my/root] followed by make and sudo make install. After that, I went back and ran cmake -H. -Bbuild to see if the dependencies were fulfilled, but I got the same output as before: cmake: /usr/local/lib/libcurl.so.4: no version information available (required by cmake) -- Check the prefix for root installation: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri -- uint8_t size: 1 bytes -- uint16_t size: 2 bytes -- uint32_t size: 4 bytes -- uint64_t size: 8 bytes -- Check for pandoc: /home/raperez/sw/ANACONDA_v5.0.1/installation_dir/bin/pandoc -- Check for Rscript: /usr/local/bin/Rscript -- Check for gunzip: /bin/gunzip -- Check for gzip: /bin/gzip -- Setting Illumina maximum read length: READ_MAXLEN 400 -- Setting Rmd quality report file: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/quality_report.Rmd -- Setting Rmd summary report file: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/summary_report.Rmd -- Setting Rmd summary filter report file: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/summary_filter_report.Rmd -- Setting Rmd summary filter report file for DS data: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/share/FastqPuri/R/summary_filter_reportDS.Rmd -- Setting compiler flags: -Wall -Wextra -O3 -march=native -std=c11 -D_DEFAULT_SOURCE -- Configuring done -- Generating done -- Build files have been written to: /media/raid/raperez/sw/FASTQPURI_v1.0.6/FastqPuri/build

Repository is updated and Rscript --slave -e "library('pheatmap')" Rscript --slave -e "library('knitr')" Rscript --slave -e "library('rmarkdown')" do not present any errors.

I'll try to talk with the server administrator to double check everything and make sure it is not our server the problem.

[PaulaAlessio]

Otherwise, edit the corresponding header file and set the variable HAVE_RPKG properly