knitr doest recognise installed packages, though no problems running chunks individualy










1















i'm having problems knitting an R markdown document. the particular chunk that's giving mt trouble uses the "tableone" package, and gives the following error:



"Error in library(tableone): there is no package called 'tableone' "



the code chunk is (if necessary i'll upload some of the the actual data):



>pt.table1<-patient.table[,-unwanted.cols]%>%tbl_df()
>catVars<-pt.table1[sapply(pt.table1,class)=="integer"]%>%colnames()
>my.tab2<-CreateTableOne(data = pt.table1,strata =
>"cerebrovascular.pt",factorVars = catVars)
>print(my.tab2)
>summary(my.tab2)


this package is properly installed,and the chunk works fine if i just run it by itself (such as with CTRL ALT C), and of course it works when ran through the console.



i have a similar problem inn a different chunk with package 'e1071'.
other packages in the rest of the code chunks work fine.



i"l appreciate any help!
thanx.
t.










share|improve this question


























    1















    i'm having problems knitting an R markdown document. the particular chunk that's giving mt trouble uses the "tableone" package, and gives the following error:



    "Error in library(tableone): there is no package called 'tableone' "



    the code chunk is (if necessary i'll upload some of the the actual data):



    >pt.table1<-patient.table[,-unwanted.cols]%>%tbl_df()
    >catVars<-pt.table1[sapply(pt.table1,class)=="integer"]%>%colnames()
    >my.tab2<-CreateTableOne(data = pt.table1,strata =
    >"cerebrovascular.pt",factorVars = catVars)
    >print(my.tab2)
    >summary(my.tab2)


    this package is properly installed,and the chunk works fine if i just run it by itself (such as with CTRL ALT C), and of course it works when ran through the console.



    i have a similar problem inn a different chunk with package 'e1071'.
    other packages in the rest of the code chunks work fine.



    i"l appreciate any help!
    thanx.
    t.










    share|improve this question
























      1












      1








      1








      i'm having problems knitting an R markdown document. the particular chunk that's giving mt trouble uses the "tableone" package, and gives the following error:



      "Error in library(tableone): there is no package called 'tableone' "



      the code chunk is (if necessary i'll upload some of the the actual data):



      >pt.table1<-patient.table[,-unwanted.cols]%>%tbl_df()
      >catVars<-pt.table1[sapply(pt.table1,class)=="integer"]%>%colnames()
      >my.tab2<-CreateTableOne(data = pt.table1,strata =
      >"cerebrovascular.pt",factorVars = catVars)
      >print(my.tab2)
      >summary(my.tab2)


      this package is properly installed,and the chunk works fine if i just run it by itself (such as with CTRL ALT C), and of course it works when ran through the console.



      i have a similar problem inn a different chunk with package 'e1071'.
      other packages in the rest of the code chunks work fine.



      i"l appreciate any help!
      thanx.
      t.










      share|improve this question














      i'm having problems knitting an R markdown document. the particular chunk that's giving mt trouble uses the "tableone" package, and gives the following error:



      "Error in library(tableone): there is no package called 'tableone' "



      the code chunk is (if necessary i'll upload some of the the actual data):



      >pt.table1<-patient.table[,-unwanted.cols]%>%tbl_df()
      >catVars<-pt.table1[sapply(pt.table1,class)=="integer"]%>%colnames()
      >my.tab2<-CreateTableOne(data = pt.table1,strata =
      >"cerebrovascular.pt",factorVars = catVars)
      >print(my.tab2)
      >summary(my.tab2)


      this package is properly installed,and the chunk works fine if i just run it by itself (such as with CTRL ALT C), and of course it works when ran through the console.



      i have a similar problem inn a different chunk with package 'e1071'.
      other packages in the rest of the code chunks work fine.



      i"l appreciate any help!
      thanx.
      t.







      r-markdown






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked Nov 14 '18 at 13:41









      Tomer MannTomer Mann

      61




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