spectral-cockpit / opusreader2

Read OPUS binary files from Fourier-Transform Infrared (FT-IR) spectrometers of the company Bruker Optics GmbH & Co. in base R
https://spectral-cockpit.github.io/opusreader2/
MIT License
18 stars 2 forks source link

Fix and prettify package #4

Closed philipp-baumann closed 2 years ago

philipp-baumann commented 2 years ago

── GP opusreader2 ───────────────────────────────────────

It is good practice to

✖ write unit tests for all functions, and all package code in general. 0% of code lines are covered by test cases.

R/create_dataset.R:2:NA
R/create_dataset.R:3:NA
R/create_dataset.R:4:NA

✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your lines shorter than 80 characters

R/old_opus_reader.R:11:81
R/old_opus_reader.R:20:81
R/old_opus_reader.R:22:81
R/old_opus_reader.R:31:81
R/old_opus_reader.R:32:81
... and 50 more lines

✖ avoid 1:length(...), 1:nrow(...), 1:ncol(...), 1:NROW(...) and 1:NCOL(...) expressions. They are error prone and result 1:0 if the expression on the right hand side is zero. Use seq_len() or seq_along() instead.

R/old_opus_reader.R:330:37
R/old_opus_reader.R:331:33
R/old_opus_reader.R:332:37
R/old_opus_reader.R:333:37
R/old_opus_reader.R:334:41

✖ fix this R CMD check WARNING: Found the following files with non-portable file names: inst/extdata/test_data/629266_1TP A-1_C1.0 inst/extdata/test_data/629266_1TP A-1_D1.0 These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ✖ fix this R CMD check WARNING: Found the following significant warnings: Warning: no source files found See ‘/tmp/Rtmp1oK0JC/file3ec6344fd1482/opusreader2.Rcheck/00install.out’ for details. ✖ fix this R CMD check WARNING: LaTeX errors when creating PDF version. This typically indicates Rd problems. ✖ fix this R CMD check ERROR: Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -Rf /tmp/RtmpHfpgYv/Rd2pdf3eedc1d27c744' ✖ fix this R CMD check WARNING: Found the following significant warnings: Warning: no source files found See ‘/tmp/Rtmp1oK0JC/file3ec6344fd1482/opusreader2.Rcheck/00install.out’ for details. ✖ fix this R CMD check WARNING: Subdirectory ‘src’ contains: bruker_opus_filereader.py These are unlikely file names for src files. ─────────────────────────────────────────────────────────