r3fang
commented
5 years ago can you reinstall “rhdf5” package and its dependencies. It seems that the installation of this package failed
-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego
On Aug 28, 2019, at 2:45 PM, yasserIRCM notifications@github.com wrote:
Hi there
I have an error message that looks like this after running the very first command on your analysis pipeline
Epoch: reading the barcode session ... [1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap" [1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap" Error in data.frame(barcode, TN, UM, PP, UQ, CM) : arguments imply differing number of rows: 0, 6641 In addition: Warning messages: 1: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 2: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 3: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 4: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 5: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 6: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 7: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
Show Traceback
Rerun with Debug Error in data.frame(barcode, TN, UM, PP, UQ, CM) : arguments imply differing number of rows: 0, 6641
on the other, we have updated the rhdf5 package to 2.29.2 and Rhdf5lib to 1.7.4
and we are still getting the same error. also, we tried to troubleshoot by using your snap files but we can't download them (we can see them but not download them).
please let us know how we can fix this.
regards
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yasserIRCM
Hi there
I have an error message that looks like this after running the very first command on your analysis pipeline
Epoch: reading the barcode session ... [1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap" [1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap" Error in data.frame(barcode, TN, UM, PP, UQ, CM) : arguments imply differing number of rows: 0, 6641 In addition: Warning messages: 1: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 2: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 3: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 4: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 5: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 6: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 7: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
Show Traceback
Rerun with Debug Error in data.frame(barcode, TN, UM, PP, UQ, CM) : arguments imply differing number of rows: 0, 6641
on the other, we have updated the rhdf5 package to 2.29.2 and Rhdf5lib to 1.7.4
and we are still getting the same error. also, we tried to troubleshoot by using your snap files but we can't download them (we can see them but not download them).
please let us know how we can fix this.
regards