I do not know how to solve it please help me
julia> using DataFrames
julia> readtable("/home/ronald/Documentos/csv/model.csv")
Error showing value of type DataFrames.DataFrame:
ERROR: type TypeName has no field wrapper
in display(::Media.DisplayHook, ::DataFrames.DataFrame) at /home/ronald/.julia/v0.6/Media/src/compat.jl:9
in display(::DataFrames.DataFrame) at ./multimedia.jl:184
in print_response(::Base.Terminals.TTYTerminal, ::Any, ::Void, ::Bool, ::Bool, ::Void) at ./REPL.jl:156
in print_response(::Base.REPL.LineEditREPL, ::Any, ::Void, ::Bool, ::Bool) at ./REPL.jl:141
in (::Base.REPL.##22#23{Bool,Base.REPL.##33#42{Base.REPL.LineEditREPL,Base.REPL.REPLHistoryProvider},Base.REPL.LineEditREPL,Base.LineEdit.Prompt})(::Base.LineEdit.MIState, ::Base.AbstractIOBuffer{Array{UInt8,1}}, ::Bool) at ./REPL.jl:654
in run_interface(::Base.Terminals.TTYTerminal, ::Base.LineEdit.ModalInterface) at ./LineEdit.jl:1579
in run_frontend(::Base.REPL.LineEditREPL, ::Base.REPL.REPLBackendRef) at ./REPL.jl:931
in run_repl(::Base.REPL.LineEditREPL, ::Base.##964#965) at ./REPL.jl:190
in _start() at ./client.jl:377
screenshot
Related
In my toy package, I have defined %+% operator as an alias to paste0(). Trying to reduce interference with other packages, I realized it the following way:
`%+%` <- function(...) UseMethod("%+%")
`%+%.character` <- paste0
`%+%.numeric` <- paste0
`%+%.default` <- function (arg1, arg2){
e <- parent.env(getEnvByName(.GlobalEnv,'package:mypackagename'));
if (exists('%+%', envir = e)) get('%+%',envir = e)(arg1,arg2);
}
i.e. I override it only for character and numeric arguments, otherwise it tries to find if the method was previously defined.
It was working just fine until recently when it started giving an error:
'a' %+% 'b'
# Error in UseMethod("%+%") :
# no applicable method for '%+%' applied to an object of class "character"
It only fails when called outside of the package. If I define a function within the package, it works correctly:
# testab2() is defined in R file as a part of the package:
testab2 <- function(inpA, inpB){
print (inpA %+% inpB)
}
# when called outside of the package:
testab2('a','b')
# ab
I am pretty sure I didn't change anything in my code, so I'm wondering if it could be caused by R update. What could have changed and how to make it work back?
P.S. getEnvByName() is my helper function that searches for an object in parent environments:
getEnvByName <- function(inpEnv=.GlobalEnv, lookFor){
e <- inpEnv;
while (environmentName(e) != 'R_EmptyEnv' & environmentName(e)!=lookFor) e <- parent.env(e);
if (environmentName(e) != lookFor) return(NULL);
return(e);
}
And the exporting was done by the following lines in the NAMESPACE file:
exportPattern("^[[:alpha:]]+")
exportPattern("%.*%")
export("%+%.default")
export("%+%.character")
P.P.S. sessionInfo:
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
system code page: 1251
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] vautils_0.1.1.105 magrittr_1.5 data.table_1.13.0
loaded via a namespace (and not attached):
[1] dplyr_1.0.2 crayon_1.3.4 grid_4.0.2 R6_2.4.1 lifecycle_0.2.0 gtable_0.3.0
[7] scales_1.1.1 ggplot2_3.3.2 pillar_1.4.6 rlang_0.4.7 rstudioapi_0.11 generics_0.0.2
[13] vctrs_0.3.4 ellipsis_0.3.1 tools_4.0.2 glue_1.4.2 purrr_0.3.4 munsell_0.5.0
[19] compiler_4.0.2 pkgconfig_2.0.3 colorspace_1.4-1 tidyselect_1.1.0 tibble_3.0.3
To export S3 methods, your NAMESPACE file needs to (in your case) contain the following declarations:
export(`%+%`)
S3method(`%+%`, default)
S3method(`%+%`, character)
S3method(`%+%`, numeric)
That is, export the %+% generic, and declare S3 methods for the methods.
Better yet, instead of manually editing the NAMESPACE file use ‘roxygen2’, which generates the correct declarations for you based on the #export documentation tag.
I've been trying to solve a problem with the RPostgreSQL package for quite some time. My code:
path_ene <- "C:/Users/omen03/ENE"
nene <- "ene_2010_02_efm.csv"
drv <- dbDriver("PostgreSQL")
con = dbConnect(drv, user="postgres", password="mypassword",
host="localhost", port=5432, dbname="ENE")
tn = "ene_2010_02_efm";
dbRemoveTable(con,tn);
dbWriteTable(conn = con, name = tn, value = paste0(path_ene,"/",nene),
sep = ",", overwrite = FALSE))
When executing the code described above, I throw the following error:
Error in postgresqlExecStatement (conn, statement, ...):
RS-DBI driver: (could not Retrieve the result: ERROR:
Could not open file «C: /Users/omen03/ENE/ene_2010_02_efm.csv» for reading: Permission denied
HINT: COPY FROM tells the PostgreSQL server process to read a
file. You may want to use a client-side facility such as psql \ copy.
) In addition: Warning message: In postgresqlImportFile (conn, name,
value, ...): could not load data into table
when I try without specifying the file path, it throws me another error
dbRemoveTable(con,tn);
dbWriteTable(conn = con, name = tn, value = nene),
sep = ",", overwrite = FALSE))
Error in postgresqlExecStatement (conn, statement, ...): RS-DBI
driver: (could not Retrieve the result: ERROR: could not open file Â
«./ ene_2010_02_efm» for reading: No such file or directory
HINT:
COPY FROM tells the PostgreSQL server process to read a file. You may
want to use a client-side facility such as psql \ copy. ) In addition:
Warning message: In postgresqlImportFile (conn, name, value, ...):
could not load data into table
Update:
Taking into account the error message, I decided to use sql directly to insert the csv values in each of the tables in the database. For that I used a couple of functions
createEmptyTable <- function(con,tn,df) {
sql <- paste0("create table \"",tn,"\" (",paste0(collapse=',','"',names(df),'" ',sapply(df[0,],postgresqlDataType)),");");
dbSendQuery(con,sql);
invisible();
};
Taken from: How to write a table in PostgreSQL from R?
and
#tn: Table name
#c_names: column names of each table (a list)
#source: The path to each csv files
insert_data = function(tn, source){
sql = paste0('COPY ',tn,' FROM \'',paste0(path_ene,'\\',source),'\' DELIMITER \',\' CSV HEADER')
dbSendQuery(con, sql);
}
insert_data(tn[1], paste0(path_ene, "/",nene[1]))
Anyway, I still get a very similar error.
Error in postgresqlExecStatement (conn, statement, ...): RS-DBI
driver: (could not Retrieve the result: ERROR: Could not open file Â
«C: /Users/omen03/ENE/ene_2010_02_efm.csv» for reading: Permission
denied HINT: COPY FROM tells the PostgreSQL server process to read a
file. You may want to use a client-side facility such as psql \ copy.
)
My session info:
R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale: [1] LC_COLLATE=Spanish_Chile.1252 LC_CTYPE=Spanish_Chile.1252
LC_MONETARY=Spanish_Chile.1252 LC_NUMERIC=C [5]
LC_TIME=Spanish_Chile.1252
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] RPostgreSQL_0.6-2 DBI_1.0.0
foreign_0.8-71 captioner_2.2.3 kableExtra_1.1.0 wordcloud_2.6
tidytext_0.2.2 gridExtra_2.3 [9] gtable_0.3.0
readstata13_0.9.2 RColorBrewer_1.1-2 ggrepel_0.8.1 pbapply_1.4-2
srvyr_0.3.6 data.table_1.12.6 lubridate_1.7.4 [17]
stringi_1.4.3 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3
[25] ggplot2_3.2.1 tidyverse_1.3.0
loaded via a namespace (and not attached): [1] httr_1.4.1
jsonlite_1.6 viridisLite_0.3.0 splines_3.6.1 modelr_0.1.5
assertthat_0.2.1 cellranger_1.1.0 sessioninfo_1.1.1 [9]
pillar_1.4.3 backports_1.1.5 lattice_0.20-38 glue_1.3.1
digest_0.6.23 rvest_0.3.5 colorspace_1.4-1 htmltools_0.4.0
[17] Matrix_1.2-17 survey_3.36 pkgconfig_2.0.3 broom_0.5.2
haven_2.2.0 scales_1.1.0 webshot_0.5.2 generics_0.0.2
[25] withr_2.1.2 lazyeval_0.2.2 cli_2.0.0
survival_2.44-1.1 magrittr_1.5 crayon_1.3.4 readxl_1.3.1
evaluate_0.14 [33] tokenizers_0.2.1 janeaustenr_0.1.5 fs_1.3.1
fansi_0.4.0 nlme_3.1-140 SnowballC_0.6.0 xml2_1.2.2
tools_3.6.1 [41] hms_0.5.2 mitools_2.4
lifecycle_0.1.0 munsell_0.5.0 reprex_0.3.0 compiler_3.6.1
rlang_0.4.2 grid_3.6.1 [49] rstudioapi_0.10
rmarkdown_1.18 R6_2.4.1 knitr_1.26 zeallot_0.1.0
parallel_3.6.1 Rcpp_1.0.3 vctrs_0.2.1 [57]
dbplyr_1.4.2 tidyselect_0.2.5 xfun_0.11
Finally, I found the answer by looking for the problem of directly importing data into postgresql. It was enough to change the configuration of the folder containing the .csv files.
I reproduce this answer that was the one I finally used.
Right click the folder containing the data file(s) that permission was denied to and then click Properties.
In the Folder's Properties window, select the Security tab.
Click the Edit button. In the "Permissions for the folder" window that opened, click the Add... button.
Type Everyone into the "Enter the object names to select" text area box.
Click OK and the window will close.
I am trying to get Julia working in colab. I want to mount gdrive to colab just like in IPython when using IJulia. In ipython I can do it as follows:
from google.colab import drive
drive.mount('/content/gdrive')
I tried following:
using PyCall
clb = pyimport("google")
clb.colab.drive.mount("/content/gdrive")
------------------------------------------------------------------------------------
Warning: Password input may be echoed.
Go to this URL in a browser: https://accounts.google.com/o/oauth2/auth?client_id=...
Enter your authorization code:
PyError ($(Expr(:escape, :(ccall(#= /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44 =# #pysym(:PyObject_Call), PyPtr, (PyPtr, PyPtr, PyPtr), o, pyargsptr, kw))))) <class 'EOFError'>
EOFError()
File "/usr/local/lib/python3.6/dist-packages/google/colab/drive.py", line 234, in mount
fifo_file.write(_getpass.getpass(auth_prompt) + '\n')
File "/usr/lib/python3.6/getpass.py", line 91, in unix_getpass
passwd = fallback_getpass(prompt, stream)
File "/usr/lib/python3.6/getpass.py", line 126, in fallback_getpass
return _raw_input(prompt, stream)
File "/usr/lib/python3.6/getpass.py", line 148, in _raw_input
raise EOFError
Stacktrace:
[1] pyerr_check at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:60 [inlined]
[2] pyerr_check at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:64 [inlined]
[3] macro expansion at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:84 [inlined]
[4] __pycall!(::PyObject, ::Ptr{PyCall.PyObject_struct}, ::PyObject, ::Ptr{Nothing}) at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44
[5] _pycall!(::PyObject, ::PyObject, ::Tuple{String}, ::Int64, ::Ptr{Nothing}) at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:29
[6] #call#111 at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:11 [inlined]
[7] (::PyObject)(::String) at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:89
[8] top-level scope at In[9]:3
using PyCall
py"""
from google.colab import drive
drive.mount('/content/gdrive')
"""
cd("/content/gdrive/My\ Drive")
------------------------------------------------------------------------------------
Warning: Password input may be echoed.
Go to this URL in a browser: https://accounts.google.com/o/oauth2/auth?client_id=...
Enter your authorization code:
PyError ($(Expr(:escape, :(ccall(#= /root/.julia/packages/PyCall/ttONZ/src/pyeval.jl:39 =# #pysym(:PyEval_EvalCode), PyPtr, (PyPtr, PyPtr, PyPtr), o, globals, locals))))) <class 'EOFError'>
EOFError()
File "/root/.julia/packages/PyCall/ttONZ/src/pyeval.jl", line 2, in <module>
const Py_file_input = 257
File "/usr/local/lib/python3.6/dist-packages/google/colab/drive.py", line 234, in mount
fifo_file.write(_getpass.getpass(auth_prompt) + '\n')
File "/usr/lib/python3.6/getpass.py", line 91, in unix_getpass
passwd = fallback_getpass(prompt, stream)
File "/usr/lib/python3.6/getpass.py", line 126, in fallback_getpass
return _raw_input(prompt, stream)
File "/usr/lib/python3.6/getpass.py", line 148, in _raw_input
raise EOFError
Stacktrace:
[1] pyerr_check at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:60 [inlined]
[2] pyerr_check at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:64 [inlined]
[3] macro expansion at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:84 [inlined]
[4] pyeval_(::String, ::PyDict{String,PyObject,true}, ::PyDict{String,PyObject,true}, ::Int64, ::String) at /root/.julia/packages/PyCall/ttONZ/src/pyeval.jl:39
[5] top-level scope at /root/.julia/packages/PyCall/ttONZ/src/pyeval.jl:232
[6] top-level scope at In[10]:2
Both did not work.
One way to achieve this is to mount google drive before installing Julia, when default Runtime type is Python by running:
from google.colab import drive
drive.mount('/content/gdrive')
That way, even after Runtime type is changed to Julia, google drive remains mounted until you change Hardware acceleration or session is lost.
I am trying to load an image using images. I get the following error:
Error showing value of type Array{RGBA{Normed{UInt8,8}},2}:
ERROR: ArgumentError: broadcasting over dictionaries and `NamedTuple`s is reserved
I call
julia> using FileIO
julia> using Images
julia> img_holder = load("zone-map.png")
Error showing value of type Array{RGBA{Normed{UInt8,8}},2}:
ERROR: ArgumentError: broadcasting over dictionaries and `NamedTuple`s is reserved
Stacktrace: etc. etc. etc.
Any thoughts on how to fix that?
Edit: I am getting the same error when I run the example from here: https://juliaimages.org/latest/function_reference/#ImageTransformations.imresize
So, maybe there's something wrong with my install? Here is the full stack track:
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.0.3 (2018-12-18)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> using Images
[ Info: Recompiling stale cache file /Users/logankilpatrick/.julia/compiled/v1.0/Images/H8Vxc.ji for Images [916415d5-f1e6-5110-898d-aaa5f9f070e0]
WARNING: Method definition _bcs1(Any, Any) in module Broadcast at broadcast.jl:439 overwritten in module ImageFiltering at /Users/logankilpatrick/.julia/packages/ImageFiltering/y5YkM/src/ImageFiltering.jl:28.
julia> using TestImages
julia> img = testimage("lena_gray_256")
Error showing value of type Array{Gray{Normed{UInt8,8}},2}:
ERROR: ArgumentError: broadcasting over dictionaries and `NamedTuple`s is reserved
Stacktrace:
[1] broadcastable(::Dict{String,Any}) at ./broadcast.jl:618
[2] broadcasted(::Function, ::Dict{String,Any}, ::Int64) at ./broadcast.jl:1171
[3] plotsize() at /Users/logankilpatrick/.julia/packages/Atom/W03fL/src/frontend.jl:21
[4] plotpane_io_ctx(::Base.GenericIOBuffer{Array{UInt8,1}}) at /Users/logankilpatrick/.julia/packages/Atom/W03fL/src/display/showdisplay.jl:5
[5] displayinplotpane(::Array{Gray{Normed{UInt8,8}},2}) at /Users/logankilpatrick/.julia/packages/Atom/W03fL/src/display/showdisplay.jl:68
[6] display(::Atom.JunoDisplay, ::Array{Gray{Normed{UInt8,8}},2}) at /Users/logankilpatrick/.julia/packages/Atom/W03fL/src/display/showdisplay.jl:102
[7] display(::Any) at ./multimedia.jl:287
[8] #invokelatest#1 at ./essentials.jl:697 [inlined]
[9] invokelatest at ./essentials.jl:696 [inlined]
[10] print_response(::IO, ::Any, ::Any, ::Bool, ::Bool, ::Any) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:154
[11] print_response(::REPL.AbstractREPL, ::Any, ::Any, ::Bool, ::Bool) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:139
[12] (::getfield(REPL, Symbol("#do_respond#40")){Bool,getfield(Atom, Symbol("##172#173")),REPL.LineEditREPL,REPL.LineEdit.Prompt})(::Any, ::Any, ::Any) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:713
[13] #invokelatest#1 at ./essentials.jl:697 [inlined]
[14] invokelatest at ./essentials.jl:696 [inlined]
[15] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:2273
[16] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:1034
[17] run_repl(::REPL.AbstractREPL, ::Any) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:191
[18] (::getfield(Base, Symbol("##718#720")){Bool,Bool,Bool,Bool})(::Module) at ./client.jl:355
[19] #invokelatest#1 at ./essentials.jl:697 [inlined]
[20] invokelatest at ./essentials.jl:696 [inlined]
[21] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:339
[22] exec_options(::Base.JLOptions) at ./client.jl:277
[23] _start() at ./client.jl:425
This happens when there's a mismatch between the version of Atom.jl and julia-client (the Atom package).
Please make sure you're on at least v0.11.0 of Atom.jl when using julia-client 0.11.x -- it's a good idea to match minor versions in general. You should also be getting a warning like this:
Hello Bioconductor users,
I am playing around with ChipDb classes, in particular the illuminaHumanv4.db package. I am simply trying to create a table of annotations from that db using the select() method, as described in the help section.
I believe the only library needed to test this is
library("illuminaHumanv4.db")
The cols() function works fine
> cols(illuminaHumanv4.db)
[1] "PROBEID" "ENTREZID" "PFAM" "IPI" "PROSITE" "ACCNUM" "ALIAS" "CHR" "CHRLOC" "CHRLOCEND"
[11] "ENZYME" "MAP" "PATH" "PMID" "REFSEQ" "SYMBOL" "UNIGENE" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
[21] "GENENAME" "UNIPROT" "GO" "EVIDENCE" "ONTOLOGY" "GOALL" "EVIDENCEALL" "ONTOLOGYALL" "OMIM" "UCSCKG"
The keytypes() function works fine too
> keytypes(illuminaHumanv4.db)
[1] "ENTREZID" "PFAM" "IPI" "PROSITE" "ACCNUM" "ALIAS" "CHR" "CHRLOC" "CHRLOCEND" "ENZYME"
[11] "MAP" "PATH" "PMID" "REFSEQ" "SYMBOL" "UNIGENE" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS" "GENENAME"
[21] "UNIPROT" "GO" "EVIDENCE" "ONTOLOGY" "GOALL" "EVIDENCEALL" "ONTOLOGYALL" "PROBEID" "OMIM" "UCSCKG"
However, when I run the keys() function, I am getting the following error
> keys(illuminaHumanv4.db)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘keys’ for signature ‘"ChipDb"’
According to the documentation, the ChipDb class should inherit this function from the AnnotationDb class. This causes a error when I try to run the select() function, since one of the arguments to pass is generated by the keys() function.
I have updated my environment (R 3.0.1, bioconductor 2.12) and all my packages and here is my sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid splines parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu95av2.db_2.9.0 BiocInstaller_1.10.2 gplots_2.11.3 KernSmooth_2.23-10 caTools_1.14 gdata_2.13.2
[7] gtools_3.0.0 hash_2.2.6 shiny_0.6.0 GO.db_2.9.0 illuminaHumanv4.db_1.18.0 org.Hs.eg.db_2.9.0
[13] RSQLite_0.11.4 DBI_0.2-7 annotate_1.38.0 AnnotationDbi_1.22.6 genefilter_1.42.0 WGCNA_1.27-1
[19] doParallel_1.0.3 iterators_1.0.6 foreach_1.4.1 MASS_7.3-27 reshape_0.8.4 plyr_1.8
[25] cluster_1.14.4 Hmisc_3.12-2 survival_2.37-4 flashClust_1.01-2 dynamicTreeCut_1.21 impute_1.34.0
[31] Biobase_2.20.1 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] AnnotationForge_1.2.2 bitops_1.0-5 codetools_0.2-8 compiler_3.0.1 digest_0.6.3 httpuv_1.0.6.3 IRanges_1.18.2
[8] lattice_0.20-15 Rcpp_0.10.4 RJSONIO_1.0-3 stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 xtable_1.7-1
Let me know if anyone has run in the same problem recently.
Thank you!