An error occurs when removing swapped molecules

[yeroslaviz]

when working on section 15.5 I get the following error when trying to identify the swappedDrops() samples. running teh commad

after.mat <- swappedDrops(swap.files, get.swapped=TRUE)

gives this error:

Error detected in HDF5 (1.10.6) thread 0:
  #000: H5F.c line 509 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 1498 in H5F_open(): unable to open file: time = Mon Feb  1 17:06:00 2021
, name = '~/Library/Caches/ExperimentHub/b5c644a7a8a_3761', tent_flags = 0
    major: File accessibilty
    minor: Unable to open file
  #002: H5FD.c line 734 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #003: H5FDsec2.c line 346 in H5FD_sec2_open(): unable to open file: name = '~/Library/Caches/ExperimentHub/b5c644a7a8a_3761', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
    major: File accessibilty
    minor: Unable to open file

my swap.files object is this

> swap.files
                                                A1                                                 B1 
 "~/Library/Caches/ExperimentHub/b5c644a7a8a_3761" "~/Library/Caches/ExperimentHub/b5c635b2fc39_3762" 
                                                C1                                                 D1 
"~/Library/Caches/ExperimentHub/b5c679cd1db9_3763"  "~/Library/Caches/ExperimentHub/b5c695a9b28_3764" 
                                                E1                                                 F1 
"~/Library/Caches/ExperimentHub/b5c61b8063e4_3765"  "~/Library/Caches/ExperimentHub/b5c6a1e1bd7_3766" 
                                                G1                                                 H1 
"~/Library/Caches/ExperimentHub/b5c63eb5c571_3767"  "~/Library/Caches/ExperimentHub/b5c6fb59de1_3768" 

Any ideas, where the problem is?

thanks

Assa

[LTLA]

This is probably caused by an update to the rappdirs package where they started reporting paths with ~ in them. HDF5 doesn't know how to deal with tildes because they haven't been expanded to the usual, e.g., /home/user/<username> or whatever it is on your system. The latest DropletUtils master contains a fix; see if it works for you.

[LTLA]

I'm going to assume this is fixed; changes have been pushed to BioC-devel and release, DropletUtils v1.10.2.

[yeroslaviz]

Hi, sorry i didn't answer earlier, but I was otherwise busy. I'm working on an iMac Catalina. I have installed the newest version from the devel repository (1.11.9) but now the package doesn't work and i keep getting this message

Error: package or namespace load failed for 'DropletUtils': object 'whichNonZero' is not exported by 'namespace:beachmat'

So I have downloaded the newest version of beachmat from the devel repository, but couldn't install it, because of this error:

Error: object ‘DummyArrayGrid’ is not exported by 'namespace:DelayedArray'
Execution halted
ERROR: lazy loading failed for package ‘beachmat’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat’

So again I tried to install the DelayedArray package (0.17.7) This was done without a problem, but a new try to install beachmat again resulted in this

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/DelayedArray/libs/DelayedArray.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/DelayedArray/libs/DelayedArray.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libR.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DelayedArray/libs/DelayedArray.so
  Reason: image not found
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘beachmat’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat’

So I don't know what to do next. I'll just try to modify to the full path to the files, if possible and see if it works there.

any ideas about the newer version?

thanks Assa

[LTLA]

Whoops, meant 1.10.3. Try resetting your installation to be BiocManager::valid() and installing from the RELEASE_3_12 branch of DropletUtils. That updated version should also pop out soon in Bioconductor release.

[yeroslaviz]

Thanks. I'll keep that in mind the next time i encounter the problem. For now I just made the full path for the file available, so the ~ is not there anymore.