Can't find raw files from R script in downloads

[grace-ac]

I can't find the .raw files that should have been put in the downloads on this computer.

What I could find, was this, and the time stamp matches when I executed the R script:

[laurahspencer]

Are you using Woodpecker? I may have moved them to the trash while cleaning up files. Also, FYI I changed the script to download in your current working directory to make it more universa.

On Tue, Oct 24, 2017 at 11:20 AM grace-ac notifications@github.com wrote:

I can't find the .raw files that should have been put in the downloads on this computer.

What I could find, was this, and the time stamp matches when I executed the R script: [image: capture] https://user-images.githubusercontent.com/14934314/31960564-0c2c7de6-b8ad-11e7-8d19-f697fa0daf4d.PNG

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[grace-ac]

Ah, ok. I'm using the one in 228 (Swan). I'll check the working directory.

[grace-ac]

This is all I can seem to find:

It matches the name that the RScript says it will be called:

[sr320]

Here is a screen cast showing the problems in the Step 1 of https://github.com/RobertsLab/Paper-DNR-Geoduck-Proteomics/blob/master/notebooks/SRM/00-Download-raw-data.md

http://d.pr/v/sXPWZy

Seems like forward slashes are problem? and nothing downloads

(at least you can see my logic if it is faulty)

[laurahspencer]

I updated the first couple lines of the script, removing the first /

 dir.create("2017-Geoduck-SRM-raw/")   
 setwd("2017-Geoduck-SRM-raw/")

This revised script worked on Woodpecker, so hopefully @grace-ac it will work for you too?

[sr320]

It will likely not..... see my screencast

That is a needed correction but the next block fails....

[kubu4]

Downloads fail on Ubuntu (related to package installs; never actually get to attempting downloads). Error messages are listed below (too long for screen caps). This is on R 3.2.3.

Provides more support that all of this should be contained in a Gti repo. Someone downloads entire repo and has all the files. R script then uses relative paths to files within that repo.

• installing source package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containinglibcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing:
• deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
• rpm: libcurl-devel (Fedora, CentOS, RHEL)

• csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

  ERROR: configuration failed for package ‘curl’

• removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/curl’ Warning in install.packages : installation of package ‘curl’ had non-zero exit status
• installing source package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked Using PKG_CFLAGS= ------------------------- ANTICONF ERROR --------------------------- Configuration failed because openssl was not found. Try installing:
• deb: libssl-dev (Debian, Ubuntu, etc)
• rpm: openssl-devel (Fedora, CentOS, RHEL)
• csw: libssl_dev (Solaris)

• brew: openssl@1.1 (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

  ERROR: configuration failed for package ‘openssl’

• removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/openssl’ Warning in install.packages : installation of package ‘openssl’ had non-zero exit status
• installing source package ‘praise’ ... package ‘praise’ successfully unpacked and MD5 sums checked R inst preparing package for lazy loading ** help * installing help indices building package indices ** testing if installed package can be loaded
• DONE (praise)
• installing source package ‘rex’ ... package ‘rex’ successfully unpacked and MD5 sums checked R inst preparing package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded
• DONE (rex)
• installing source package ‘stringr’ ... package ‘stringr’ successfully unpacked and MD5 sums checked R data moving datasets to lazyload DB inst preparing package for lazy loading help installing help indices building package indices installing vignettes ** testing if installed package can be loaded
• DONE (stringr) ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
• removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/httr’ Warning in install.packages : installation of package ‘httr’ had non-zero exit status
• installing source package ‘testthat’ ... package ‘testthat’ successfully unpacked and MD5 sums checked libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c label.c -o label.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reassign.c -o reassign.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-catch.cpp -o test-catch.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-example.cpp -o test-example.o g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-runner.cpp -o test-runner.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib/R/lib -lR installing to /home/samb/R/x86_64-pc-linux-gnu-library/3.2/testthat/libs R inst preparing package for lazy loading help * installing help indices building package indices ** testing if installed package can be loaded
• DONE (testthat) ERROR: dependency ‘httr’ is not available for package ‘covr’
• removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/covr’ Warning in install.packages : installation of package ‘covr’ had non-zero exit status

The downloaded source packages are in ‘/tmp/RtmpUhCsyJ/downloaded_packages’

install.packages("curl", dep=TRUE) Installing package into ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2’ (as ‘lib’ is unspecified) also installing the dependency ‘webutils’

--2017-10-24 17:38:45-- https://cran.rstudio.com/src/contrib/webutils_0.6.tar.gz Resolving cran.rstudio.com (cran.rstudio.com)... 13.32.207.112 Connecting to cran.rstudio.com (cran.rstudio.com)|13.32.207.112|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 22694 (22K) [application/x-gzip] Saving to: ‘/tmp/RtmpUhCsyJ/downloaded_packages/webutils_0.6.tar.gz’

 0K .......... .......... ..                              100%  342M=0s

2017-10-24 17:38:45 (342 MB/s) - ‘/tmp/RtmpUhCsyJ/downloaded_packages/webutils_0.6.tar.gz’ saved [22694/22694]

--2017-10-24 17:38:45-- https://cran.rstudio.com/src/contrib/curl_3.0.tar.gz Resolving cran.rstudio.com (cran.rstudio.com)... 13.32.207.112 Connecting to cran.rstudio.com (cran.rstudio.com)|13.32.207.112|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 412212 (403K) [application/x-gzip] Saving to: ‘/tmp/RtmpUhCsyJ/downloaded_packages/curl_3.0.tar.gz’

 0K .......... .......... .......... .......... .......... 12% 7.25M 0s
50K .......... .......... .......... .......... .......... 24% 8.07M 0s

100K .......... .......... .......... .......... .......... 37% 12.1M 0s 150K .......... .......... .......... .......... .......... 49% 7.33M 0s 200K .......... .......... .......... .......... .......... 62% 12.0M 0s 250K .......... .......... .......... .......... .......... 74% 7.54M 0s 300K .......... .......... .......... .......... .......... 86% 6.02M 0s 350K .......... .......... .......... .......... .......... 99% 10.0M 0s 400K .. 100% 4865G=0.05s

2017-10-24 17:38:45 (8.36 MB/s) - ‘/tmp/RtmpUhCsyJ/downloaded_packages/curl_3.0.tar.gz’ saved [412212/412212]

• installing source package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containinglibcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing:
  • deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
  • rpm: libcurl-devel (Fedora, CentOS, RHEL)

  • csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

    ERROR: configuration failed for package ‘curl’

• removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/curl’ Warning in install.packages : installation of package ‘curl’ had non-zero exit status ERROR: dependency ‘curl’ is not available for package ‘webutils’
• removing ‘/home/samb/R/x86_64-pc-linux-gnu-library/3.2/webutils’ Warning in install.packages : installation of package ‘webutils’ had non-zero exit statu

[laurahspencer]

@sr320 can you try running the entire script now that I've made the edit to the first few lines? In your screencast you did not run the whole script, which is required to actually download the files. Most of the lines in this script create objects in R, to be used by R, to download the correct urls and save with the correct names.

@kubu4 does the script work in RStudio using Ubuntu?

[kubu4]

No - it fails on installing cURL. Although, it proceeds through the script and spits out "FALSE" (because it couldn't install cURL).

See my comment above.

[grace-ac]

Just used the new script in the notebook and it worked!