Hi Simon,

I've been struggling with images that are "partially corrupted" - that is, part of the image is cut off by a large black or grey area (see example image, here). If I run "readJPEG" on this image like this:

img <- readJPEG("2017-08-30 00-17-42 M 1_5.JPG")

the output is:

JPEG decompression: Corrupt JPEG data: premature end of data segment.

As far as I can tell, this "message" is not actually a message or a warning, which makes it really difficult to do error checking or to capture that message or warning (for example, in tryCatch). For a more fulsome explanation of why this is troublesome, consider my question at stack overflow (here), if you're interested.

In any case, is it possible to change the function (or provide a similar one, like readJPEG2) that outputs that explanatory text as a message or warning?

Checked on

• R 3.6.3 and R 4.0 beta
• SDK 10.15 and SDK 10.13

The jpeg lib is installed and linked via homebrew.

install.packages("jpeg", type = "source")
#> Installing package into '/Users/pjs/Library/R/4.0/library'
#> (as 'lib' is unspecified)
* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
ccache clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk   -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c read.c -o read.o
In file included from read.c:1:
./rjcommon.h:11:10: fatal error: 'jpeglib.h' file not found
#include <jpeglib.h>
         ^~~~~~~~~~~
1 error generated.
make: *** [read.o] Error 1
ERROR: compilation failed for package ‘jpeg’
* removing ‘/Users/pjs/Library/R/4.0/library/jpeg’
* restoring previous ‘/Users/pjs/Library/R/4.0/library/jpeg’

The downloaded source packages are in
        ‘/private/var/folders/w5/1wdhg7nd4zj7td7_pkgrl4fm0000gn/T/RtmpQjlll2/downloaded_packages’
Warning message:
In install.packages("jpeg", type = "source") :

^{Created on 2020-04-13 by the reprex package (v0.3.0)}

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                                   
#>  version  R version 4.0.0 beta (2020-04-12 r78209)
#>  os       macOS Catalina 10.15.4                  
#>  system   x86_64, darwin17.0                      
#>  ui       X11                                     
#>  language (EN)                                    
#>  collate  en_US.UTF-8                             
#>  ctype    en_US.UTF-8                             
#>  tz       Europe/Berlin                           
#>  date     2020-04-13                              
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source        
#>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
#>  backports     1.1.6   2020-04-05 [1] CRAN (R 4.0.0)
#>  callr         3.4.3   2020-03-28 [1] CRAN (R 4.0.0)
#>  cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.0)
#>  crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
#>  desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
#>  devtools      2.3.0   2020-04-10 [1] CRAN (R 4.0.0)
#>  digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.0)
#>  ellipsis      0.3.0   2019-09-20 [1] CRAN (R 4.0.0)
#>  evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.0)
#>  fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
#>  fs            1.4.1   2020-04-04 [1] CRAN (R 4.0.0)
#>  glue          1.4.0   2020-04-03 [1] CRAN (R 4.0.0)
#>  highr         0.8     2019-03-20 [1] CRAN (R 4.0.0)
#>  htmltools     0.4.0   2019-10-04 [1] CRAN (R 4.0.0)
#>  knitr         1.28    2020-02-06 [1] CRAN (R 4.0.0)
#>  magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.0)
#>  memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
#>  pkgbuild      1.0.6   2019-10-09 [1] CRAN (R 4.0.0)
#>  pkgload       1.0.2   2018-10-29 [1] CRAN (R 4.0.0)
#>  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
#>  processx      3.4.2   2020-02-09 [1] CRAN (R 4.0.0)
#>  ps            1.3.2   2020-02-13 [1] CRAN (R 4.0.0)
#>  R6            2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
#>  Rcpp          1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
#>  remotes       2.1.1   2020-02-15 [1] CRAN (R 4.0.0)
#>  rlang         0.4.5   2020-03-01 [1] CRAN (R 4.0.0)
#>  rmarkdown     2.1     2020-01-20 [1] CRAN (R 4.0.0)
#>  rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
#>  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
#>  stringi       1.4.6   2020-02-17 [1] CRAN (R 4.0.0)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.0.0)
#>  testthat      2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
#>  usethis       1.6.0   2020-04-09 [1] CRAN (R 4.0.0)
#>  withr         2.1.2   2018-03-15 [1] CRAN (R 4.0.0)
#>  xfun          0.13    2020-04-13 [1] CRAN (R 4.0.0)
#>  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.0)
#> 
#> [1] /Users/pjs/Library/R/4.0/library
#> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

Hi!
I tried to install package as a part of "ggmap" installation:
devtools::install_github("s-u/jpeg")

And get the following errors

• installing source package ‘jpeg’ ...
  ** libs
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o
  In file included from read.c:1:0:
  rjcommon.h:11:21: fatal error: jpeglib.h: No such file or directory
  compilation terminated.
  /usr/lib/R/etc/Makeconf:159: recipe for target 'read.o' failed
  make: *** [read.o] Error 1
  ERROR: compilation failed for package ‘jpeg’
• removing ‘/home/andrii/R/x86_64-pc-lin

Will be glad to know how to fix it

Hi,

I'm just trying to download the package in RStudio and having mega issues. I even uninstalled R and RStudio and brought them back but to no avail. Here's what I'm getting in the console when I try to install. If there's anything I'm doing wrong, please let me know. Thanks

(as ‘lib’ is unspecified)
trying URL 'http://rforge.net/src/contrib/jpeg_0.1-9.tar.gz'
Content type 'application/x-gzip' length 18097 bytes (17 KB)
downloaded 17 KB

* installing *source* package 'jpeg' ...
** using staged installation
  checking JPEG headers and libraries
  LOCAL_SOFT does not exist, fall back to external jpeg
  cannot find current JPEG files
  attempting to download them
Error in download.file("http://www.rforge.net/jpeg/files/libjpeg-current-win.tar.gz",  : 
  cannot open destfile 'src/libjpeg-current-win.tar.gz', reason 'No such file or directory'
Execution halted

 *** ERROR: unable to find JPEG files

 They must be either in src/win32, in a tar-ball
 src/libjpeg-current-win.tar.gz or
 available via the LOCAL_SOFT R make setting.

 You can get the latest binary tar ball from
 http://www.rforge.net/jpeg/files/

ERROR: configuration failed for package 'jpeg'
* removing 'C:/Users/MadisonDC/Documents/R/win-library/4.1/jpeg'
Warning in install.packages :
  installation of package ‘jpeg’ had non-zero exit status

The downloaded source packages are in
	‘C:\Users\MadisonDC\AppData\Local\Temp\RtmpctQ5UI\downloaded_packages’

I don't think this has been documented, so just wanted to share installation instructions if libjpeg is installed in a non-standard location, on Linux at least. Enter something like the following in the shell:

export JPEG_CFLAGS=-I/path/to/libjpeg/include
export JPEG_LIBS=-L/path/to/libjpeg/lib

Make sure to substitute the libjpeg installation path.

Then within R, install the jpeg package like normal.

Hi, I am trying to install by compiling from source on R 4.0.3 on BigSur 11.2 and get this error:

ld: library not found for -ljpeg
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [qpdf.so] Error 1
ERROR: compilation failed for package `‘qpdf’```

I have libjpeg 9d installed via Homebrew. I tried to reinstall and re-start R with no success. No matter what, the error persists. Any suggestions? Thanks

I have two cat images, one in high format and one in landscape format (https://www.dropbox.com/sh/7xa9jfxlsr6wy5s/AABVZJO0GrwvuVb9qryJjCG7a?dl=0). When I read them with readJPEG the dimensions for both are the same:

jpg1 <- readJPEG("/Volumes/Vero/Data/Animals/Cat/20150805_172829743_iOS.jpg")
jpg2 <- readJPEG("/Volumes/Vero/Data/Animals/Cat/20150808_183100413_iOS.jpg")
str(jpg1)
str(jpg2)

The last two lines both print num [1:2448, 1:3264, 1:3] 0.996 0.996 0.996 0.996 0.996 ... although the first (high format) should be [1:3264 1:2448 1:3]. When I save them again with writeJPEG the landscape one looks normal (although its larger than before) and the other one is mixed up (it's rather large so I don't upload it except you would like me to).

After using jpg1_a <- aperm(jpg1, c(2, 1, 3)) and writing the image it looks normal but rotated.

Is there something wrong with the library or is it a problem with my image? (I have encountered that some other programs also have problems with photos taken by an iPhone).

Best regards,
Verena

EDIT: I looked a little further and found out that the rotation would be in the exif data (1 for "normal" and 6 for "rotated"), e.g. explained here. [http://www.daveperrett.com/articles/2012/07/28/exif-orientation-handling-is-a-ghetto/](EXIF orientation handling is a ghetto). I'm trying to figure out a way based on the [https://github.com/ironholds/exif](exif meta data) to handle my images correctly. I don't know if you will/want to include this information in your package.