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Does the function "c" have a character limit?

12 messages · David Winsemius, Ivan Krylov, Kimmo Elo +5 more

Original
core_contingency
# 
To Whom it May Concern,

I am creating a vector with the base R function "c", with many arguments 
as shown below:

 ???? $ R
 ???? > MES = c("A2M", "ABRACL", "ACADVL", "ACAP2", "ACTA2", "ACTN1", 
"ADAM19", "ADAM9", "ADAMTS5", "ADGRE5", "ADGRG6", "AEBP1", "AJUBA", 
"ALDH1A3", "AMMECR1", "ANTXR1", "ANXA1", "ANXA2", "ANXA5", "ANXA6", 
"APOE", "APP", "ARHGAP1", "ARHGEF40", "ARL1", "ARL4A", "ARMCX2", 
"ARPC1B", "ASPH", "ATP10D", "ATP1B1", "ATP2B1", "ATP2B4", "ATP6V0E1", 
"ATP8B2", "ATXN1", "B2M", "BAG3", "BGN", "BMP5", "BNC2", "BOC", 
"BTN3A2", "C1orf198", "C1orf54", "C4orf32", "C6orf120", "CALD1", "CALU", 
"CAPN2", "CAPN6", "CBFB", "CBLB", "CCDC80", "CD164", "CD44", "CD59", 
"CD63", "CDH11", "CETN2", "CFH", "CFI", "CILP", "CKAP4", "CLIC4", 
"CMTM3", "CMTM6", "CNN3", "COL11A1", "COL12A1", "COL1A1", "COL27A1", 
"COL3A1", "COL4A1", "COL4A2", "COL5A1", "COL5A2", "COL6A1", "COL6A2", 
"COL6A3", "COPA", "CPED1", "CPS1", "CRABP2", "CREB3L2", "CREG1", 
"CRELD2", "CRISPLD1", "CRTAP", "CSRP1", "CTDSP2", "CTNNA1", "CTSB", 
"CTSC", "CTSO", "CXCL12", "CYBRD1", "CYFIP1", "CYP26A1", "CYR61", 
"DCAF6", "DDOST", "DDR2", "DESI2", "DKK3", "DLC1", "DLX1", "DLX2", 
"DMD", "DNAJC1", "DNAJC10", "DNAJC3", "DNM3OS", "DPY19L1", "DSE", 
"DUSP14", "DUSP5", "DUSP6", "EDEM1", "EDNRA", "EFEMP2", "EGFR", "EGR1", 
"EGR3", "EHD2", "ELAVL1", "ELF1", "ELK3", "ELK4", "EMILIN1", "EMP1", 
"ENAH", "EPHA3", "EPS8", "ERBIN", "ERLIN1", "ERRFI1", "ETS1", "EVA1A", 
"EXT1", "EXTL2", "F2R", "F2RL2", "FAM102B", "FAM114A1", "FAM120A", 
"FAM129A", "FAM3C", "FAM43A", "FAM46A", "FAT1", "FBN1", "FBN2", "FGFR1", 
"FIBIN", "FILIP1L", "FKBP14", "FLNA", "FLRT2", "FMOD", "FN1", "FNDC3B", 
"FSTL1", "FUCA2", "FZD1", "FZD2", "FZD7", "GABRR1", "GALNT10", "GAS1", 
"GAS2", "GDF15", "GJA1", "GNAI1", "GNG12", "GNS", "GORAB", "GPC6", 
"GPR137B", "GPX8", "GRN", "GSN", "HES1", "HEXB", "HIBADH", "HIPK3", 
"HIST1H2AC", "HIST1H2BK", "HLA-A", "HLA-B", "HLA-C", "HLA-F", "HLX", 
"HNMT", "HOMER1", "HS3ST3A1", "HSP90B1", "HSPA5", "HSPB1", "HTRA1", 
"HYOU1", "ID1", "ID3", "IFI16", "IFITM2", "IFITM3", "IGF2R", "IGFBP5", 
"IGFBP6", "IL13RA1", "IL6ST", "INSIG1", "IQGAP2", "ITGA10", "ITGA4", 
"ITGAV", "ITGB1", "ITM2B", "ITM2C", "ITPR1", "ITPRIPL2", "JAK1", "JAM3", 
"KANK2", "KCNK2", "KCTD12", "KDELC2", "KDELR2", "KDELR3", "KDM5B", 
"KIAA1462", "KIF13A", "KIRREL", "KLF10", "KLF4", "KLF6", "L3HYPDH", 
"LAMB1", "LAMC1", "LAMP1", "LAPTM4A", "LASP1", "LATS2", "LEPROT", 
"LGALS1", "LHFP", "LHX8", "LIFR", "LIPA", "LITAF", "LIX1L", "LMAN1", 
"LMNA", "LOXL2", "LPP", "LRP10", "LRRC17", "LRRC8C", "LTBP1", "LUZP1", 
"MAGT1", "MAML2", "MAN2A1", "MANF", "MBD2", "MBNL1", "MBTPS1", "MEOX1", 
"MEOX2", "MEST", "MGAT2", "MGP", "MGST1", "MICAL2", "MMP2", "MOB1A", 
"MRC2", "MXRA5", "MYADM", "MYDGF", "MYL12A", "MYL12B", "MYLIP", "NANS", 
"NBR1", "NEK7", "NES", "NFIA", "NFIC", "NID1", "NID2", "NOTCH2", 
"NOTCH2NL", "NPC2", "NPTN", "NQO1", "NR3C1", "NRP1", "OGFRL1", 
"OLFML2A", "OLFML2B", "OLFML3", "OSTC", "P4HA1", "PALLD", "PAPSS2", 
"PCDH18", "PCOLCE2", "PCSK5", "PDE3A", "PDE7B", "PDGFC", "PDIA3", 
"PDIA4", "PDIA6", "PDLIM1", "PEA15", "PEAK1", "PHLDA3", "PHLDB2", 
"PHTF2", "PIAS3", "PLAGL1", "PLEKHA2", "PLEKHH2", "PLK2", "PLOD2", 
"PLOD3", "PLPP1", "PLS3", "PLSCR1", "PLSCR4", "PLXDC2", "POLR2L", 
"PON2", "POSTN", "PPIB", "PPIC", "PPT1", "PRCP", "PRDM6", "PRDX4", 
"PRDX6", "PROM1", "PRRX1", "PTBP1", "PTGER4", "PTGFRN", "PTN", "PTPN14", 
"PTPRG", "PTPRK", "PTRF", "PXDC1", "PXDN", "PYGL", "QKI", "QSOX1", 
"RAB13", "RAB29", "RAB31", "RAP1A", "RAP1B", "RBMS1", "RCN1", "RECK", 
"REST", "RGL1", "RGS10", "RGS3", "RHOC", "RHOJ", "RIN2", "RIT1", 
"RNFT1", "RNH1", "ROBO1", "ROR1", "RRBP1", "S1PR3", "SASH1", "SCPEP1", 
"SCRG1", "SDC2", "SDC4", "SDCBP", "SDF4", "SEC14L1", "SEL1L3", "SEMA3C", 
"SEMA3F", "SEPT10", "SERPINE2", "SERPINH1", "SFT2D1", "SFT2D2", "SGK1", 
"SH3BGRL", "SHC1", "SHROOM3", "SIX1", "SIX4", "SKIL", "SLC16A4", 
"SLC30A1", "SLC30A7", "SLC35F5", "SLC38A2", "SLC38A6", "SLC39A14", 
"SMAD3", "SNAI2", "SNAP23", "SOSTDC1", "SOX9", "SPARC", "SPARCL1", 
"SPATA20", "SPCS3", "SPRED1", "SPRY1", "SPRY4", "SPRY4-IT1", "SQSTM1", 
"SRPX", "SSBP4", "SSR1", "SSR3", "STAT1", "STAT3", "STEAP1", "STK38L", 
"SUCLG2", "SURF4", "SVIL", "SYDE1", "SYNJ2", "SYPL1", "TCF7L2", "TFE3", 
"TFPI", "TGFB1I1", "TGFBR2", "THBS1", "TIMP1", "TJP1")
 ???? +

For some reason, the R console does not display a ">" symbol, indicating 
that it has completed the function, but displays a "+" symbol instead, 
which indicates that the function is still waiting for more input. 
However, I believe that my syntax is correct. If I shorten my command by 
a few characters by removing the last entry, "TJP1":

 ???? $ R
 ???? > MES = c("A2M", "ABRACL", "ACADVL", "ACAP2", "ACTA2", "ACTN1", 
"ADAM19", "ADAM9", "ADAMTS5", "ADGRE5", "ADGRG6", "AEBP1", "AJUBA", 
"ALDH1A3", "AMMECR1", "ANTXR1", "ANXA1", "ANXA2", "ANXA5", "ANXA6", 
"APOE", "APP", "ARHGAP1", "ARHGEF40", "ARL1", "ARL4A", "ARMCX2", 
"ARPC1B", "ASPH", "ATP10D", "ATP1B1", "ATP2B1", "ATP2B4", "ATP6V0E1", 
"ATP8B2", "ATXN1", "B2M", "BAG3", "BGN", "BMP5", "BNC2", "BOC", 
"BTN3A2", "C1orf198", "C1orf54", "C4orf32", "C6orf120", "CALD1", "CALU", 
"CAPN2", "CAPN6", "CBFB", "CBLB", "CCDC80", "CD164", "CD44", "CD59", 
"CD63", "CDH11", "CETN2", "CFH", "CFI", "CILP", "CKAP4", "CLIC4", 
"CMTM3", "CMTM6", "CNN3", "COL11A1", "COL12A1", "COL1A1", "COL27A1", 
"COL3A1", "COL4A1", "COL4A2", "COL5A1", "COL5A2", "COL6A1", "COL6A2", 
"COL6A3", "COPA", "CPED1", "CPS1", "CRABP2", "CREB3L2", "CREG1", 
"CRELD2", "CRISPLD1", "CRTAP", "CSRP1", "CTDSP2", "CTNNA1", "CTSB", 
"CTSC", "CTSO", "CXCL12", "CYBRD1", "CYFIP1", "CYP26A1", "CYR61", 
"DCAF6", "DDOST", "DDR2", "DESI2", "DKK3", "DLC1", "DLX1", "DLX2", 
"DMD", "DNAJC1", "DNAJC10", "DNAJC3", "DNM3OS", "DPY19L1", "DSE", 
"DUSP14", "DUSP5", "DUSP6", "EDEM1", "EDNRA", "EFEMP2", "EGFR", "EGR1", 
"EGR3", "EHD2", "ELAVL1", "ELF1", "ELK3", "ELK4", "EMILIN1", "EMP1", 
"ENAH", "EPHA3", "EPS8", "ERBIN", "ERLIN1", "ERRFI1", "ETS1", "EVA1A", 
"EXT1", "EXTL2", "F2R", "F2RL2", "FAM102B", "FAM114A1", "FAM120A", 
"FAM129A", "FAM3C", "FAM43A", "FAM46A", "FAT1", "FBN1", "FBN2", "FGFR1", 
"FIBIN", "FILIP1L", "FKBP14", "FLNA", "FLRT2", "FMOD", "FN1", "FNDC3B", 
"FSTL1", "FUCA2", "FZD1", "FZD2", "FZD7", "GABRR1", "GALNT10", "GAS1", 
"GAS2", "GDF15", "GJA1", "GNAI1", "GNG12", "GNS", "GORAB", "GPC6", 
"GPR137B", "GPX8", "GRN", "GSN", "HES1", "HEXB", "HIBADH", "HIPK3", 
"HIST1H2AC", "HIST1H2BK", "HLA-A", "HLA-B", "HLA-C", "HLA-F", "HLX", 
"HNMT", "HOMER1", "HS3ST3A1", "HSP90B1", "HSPA5", "HSPB1", "HTRA1", 
"HYOU1", "ID1", "ID3", "IFI16", "IFITM2", "IFITM3", "IGF2R", "IGFBP5", 
"IGFBP6", "IL13RA1", "IL6ST", "INSIG1", "IQGAP2", "ITGA10", "ITGA4", 
"ITGAV", "ITGB1", "ITM2B", "ITM2C", "ITPR1", "ITPRIPL2", "JAK1", "JAM3", 
"KANK2", "KCNK2", "KCTD12", "KDELC2", "KDELR2", "KDELR3", "KDM5B", 
"KIAA1462", "KIF13A", "KIRREL", "KLF10", "KLF4", "KLF6", "L3HYPDH", 
"LAMB1", "LAMC1", "LAMP1", "LAPTM4A", "LASP1", "LATS2", "LEPROT", 
"LGALS1", "LHFP", "LHX8", "LIFR", "LIPA", "LITAF", "LIX1L", "LMAN1", 
"LMNA", "LOXL2", "LPP", "LRP10", "LRRC17", "LRRC8C", "LTBP1", "LUZP1", 
"MAGT1", "MAML2", "MAN2A1", "MANF", "MBD2", "MBNL1", "MBTPS1", "MEOX1", 
"MEOX2", "MEST", "MGAT2", "MGP", "MGST1", "MICAL2", "MMP2", "MOB1A", 
"MRC2", "MXRA5", "MYADM", "MYDGF", "MYL12A", "MYL12B", "MYLIP", "NANS", 
"NBR1", "NEK7", "NES", "NFIA", "NFIC", "NID1", "NID2", "NOTCH2", 
"NOTCH2NL", "NPC2", "NPTN", "NQO1", "NR3C1", "NRP1", "OGFRL1", 
"OLFML2A", "OLFML2B", "OLFML3", "OSTC", "P4HA1", "PALLD", "PAPSS2", 
"PCDH18", "PCOLCE2", "PCSK5", "PDE3A", "PDE7B", "PDGFC", "PDIA3", 
"PDIA4", "PDIA6", "PDLIM1", "PEA15", "PEAK1", "PHLDA3", "PHLDB2", 
"PHTF2", "PIAS3", "PLAGL1", "PLEKHA2", "PLEKHH2", "PLK2", "PLOD2", 
"PLOD3", "PLPP1", "PLS3", "PLSCR1", "PLSCR4", "PLXDC2", "POLR2L", 
"PON2", "POSTN", "PPIB", "PPIC", "PPT1", "PRCP", "PRDM6", "PRDX4", 
"PRDX6", "PROM1", "PRRX1", "PTBP1", "PTGER4", "PTGFRN", "PTN", "PTPN14", 
"PTPRG", "PTPRK", "PTRF", "PXDC1", "PXDN", "PYGL", "QKI", "QSOX1", 
"RAB13", "RAB29", "RAB31", "RAP1A", "RAP1B", "RBMS1", "RCN1", "RECK", 
"REST", "RGL1", "RGS10", "RGS3", "RHOC", "RHOJ", "RIN2", "RIT1", 
"RNFT1", "RNH1", "ROBO1", "ROR1", "RRBP1", "S1PR3", "SASH1", "SCPEP1", 
"SCRG1", "SDC2", "SDC4", "SDCBP", "SDF4", "SEC14L1", "SEL1L3", "SEMA3C", 
"SEMA3F", "SEPT10", "SERPINE2", "SERPINH1", "SFT2D1", "SFT2D2", "SGK1", 
"SH3BGRL", "SHC1", "SHROOM3", "SIX1", "SIX4", "SKIL", "SLC16A4", 
"SLC30A1", "SLC30A7", "SLC35F5", "SLC38A2", "SLC38A6", "SLC39A14", 
"SMAD3", "SNAI2", "SNAP23", "SOSTDC1", "SOX9", "SPARC", "SPARCL1", 
"SPATA20", "SPCS3", "SPRED1", "SPRY1", "SPRY4", "SPRY4-IT1", "SQSTM1", 
"SRPX", "SSBP4", "SSR1", "SSR3", "STAT1", "STAT3", "STEAP1", "STK38L", 
"SUCLG2", "SURF4", "SVIL", "SYDE1", "SYNJ2", "SYPL1", "TCF7L2", "TFE3", 
"TFPI", "TGFB1I1", "TGFBR2", "THBS1", "TIMP1")
 ???? >

The function now works, and returns a ">" symbol, indicating that the 
function completed successfully. The ls() function proves it:

 ???? $ R
 ???? > ls()
 ???? [1] "MES"

Is this a bug in the base R "c" function? It seems like the "c" function 
can only accept so many characters before it fails.

Thank you for your time,
core_contingency


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David Winsemius
# 
I think the restriction is not specific to `c` but rather is a limitation on the length of expressions. My foggy memory is that the limit is in the 450-500 character vicinity. Pretty sure it?s been discussed here in the past. 

? 
David. 

Sent from my iPhone
David Winsemius
#
On 7/12/22 23:26, David Winsemius wrote:
One way to get around this limitation is to create a .r file and source 
the material. I just tested with your code and it succeeded.
Ivan Krylov
# 
On Tue, 12 Jul 2022 16:36:06 -0700
core_contingency <ccontingency at gmail.com> wrote:

            

      
      
      
    

        
If I copy&paste from your message into an R session, it seems to work
for me. I think the reason for that is because what was a single long
line has been wrapped into a lot of shorter lines.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Kimmo Elo
    

    

      
      #
    

  


  

      
Hi!

Cannot reproduce this either with my R 4.2.1 on Linux. Just copy-pasted 
your expression and it works just fine.

Best,
Kimmo

ti, 2022-07-12 kello 23:39 -0700, David Winsemius kirjoitti:

            

      
      
      
    

        

      
      
    

        

      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
      #
    

  


  

      
Hello,

This is documented behavior.
 From R-intro, last line of section 1.8 [1].


Command lines entered at the console are limited4 to about 4095 bytes 
(not characters).


The number 4 in limited4 is a footnote link:


some of the consoles will not allow you to enter more, and amongst those 
which do some will silently discard the excess and some will use it as 
the start of the next line.



Prof. Ripley called the r-devel mailing list's attention to this in 
August 2006 when the limit was 1024 [2], it was then increased to the 
current 4095. I remember seeing a limit of 2048 (?) but couldn't find where.


Try creating a file with your command as only content, then run


x <- readLines("rhelp.txt")
nchar(x)
# [1] 4096


You are above the limit by 1 byte.
Standard solutions are to break the command line, in your case into at 
least 2 lines, or to source the command from file, like David proposed.


[1] 
https://cran.r-project.org/doc/manuals/R-intro.html#R-commands_003b-case-sensitivity-etc
[2] https://stat.ethz.ch/pipermail/r-devel/2006-August/038985.html


Hope this helps,

Rui Barradas


?s 00:36 de 13/07/2022, core_contingency escreveu:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ebert,Timothy Aaron
    

    

      
      #
    

  


  

      
The limits to the size of vectors, matrices, data frames, lists, or other data structure does not have a simple answer.
1) 2^31 - 1  is the maximum number of rows. https://stackoverflow.com/questions/5233769/practical-limits-of-r-data-frame#:~:text=The%20number%20is%202%5E31,start%20collecting%20several%20of%20them.
2) help(Memory) suggests that the default limit for all variables is 6 Mb. The help page tells you how to change this.
Neither of these two factors have any bearing on this problem except that your vector is not close to these limits.

I got the same result you did when I entered your vector into my system (R 4.2 in RStudio, on 64 bit Windows). I shortened it by removing the first entry and it works.

I can copy the entire line into Microsoft Word, and count the number of characters (including spaces) and I get 4089. There were seven characters in the first entry including the comma and space. If I add seven spaces between MES and the equal sign I get the original outcome. So the limit is on the number of characters in the line. You can get more entries by shortening each entry, or fewer if each entry was longer.

As others have suggested, I would break the line into two pieces and then combine the pieces.

Tim



-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Rui Barradas
Sent: Wednesday, July 13, 2022 6:36 AM
To: core_contingency <ccontingency at gmail.com>; r-help at r-project.org
Subject: Re: [R] Does the function "c" have a character limit?

[External Email]

Hello,

This is documented behavior.
 From R-intro, last line of section 1.8 [1].


Command lines entered at the console are limited4 to about 4095 bytes (not characters).


The number 4 in limited4 is a footnote link:


some of the consoles will not allow you to enter more, and amongst those which do some will silently discard the excess and some will use it as the start of the next line.



Prof. Ripley called the r-devel mailing list's attention to this in August 2006 when the limit was 1024 [2], it was then increased to the current 4095. I remember seeing a limit of 2048 (?) but couldn't find where.


Try creating a file with your command as only content, then run


x <- readLines("rhelp.txt")
nchar(x)
# [1] 4096


You are above the limit by 1 byte.
Standard solutions are to break the command line, in your case into at least 2 lines, or to source the command from file, like David proposed.


[1]
https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dintro.html-23R-2Dcommands-5F003b-2Dcase-2Dsensitivity-2Detc&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=g5cbrpfyHaIN9sXycd_-f2iDsOcbuzLe2u3KjvQNm-0&e=
[2] https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_r-2Ddevel_2006-2DAugust_038985.html&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=B1YSca31vHlpy9WJG8o0MBTh7bX4v7M61eWfQ4tmdog&e=


Hope this helps,

Rui Barradas


?s 00:36 de 13/07/2022, core_contingency escreveu:

            

      
      
      
    

        

      
      
    

        
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=x5SJbPFsoqRiJYh7Y5B0QDKio2Wy4Je38lBBi99AbAE&e=
PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=lCG5D1ItMs8G_wkshvm4nBaVq4Ehy_zyq5mnp2zpt2Y&e=
and provide commented, minimal, self-contained, reproducible code.

  
  


  


      

    

    

      
      

        


  

        

      Richard O'Keefe
    

    

      
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Breaking up the *line* doesn't mean breaking up the *command*.
For example,
x <- c(
    "FOOBAR", # 1
    ...
    "FOOBAR", # 4999
    "UGGLE")
works fine, with source(..), with "R -f ...", and other ways.
Each *line* is short, but it's still one *command*.

I'd probably put that much data in a file, myself,
but R doesn't mind.

        
On Thu, 14 Jul 2022 at 01:21, Ebert,Timothy Aaron <tebert at ufl.edu> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
      #
    

  


  

      
Hello,

The original command has spaces in it. If they are removed its total 
length goes down to 3649 bytes (or characters, in this case it's the 
same). With this length the command is expected to work without further 
worries. And it does, I have just tried it.


MES=c("A2M","ABRACL","ACADVL","ACAP2","ACTA2","ACTN1","ADAM19","ADAM9","ADAMTS5","ADGRE5","ADGRG6","AEBP1","AJUBA","ALDH1A3","AMMECR1","ANTXR1","ANXA1","ANXA2","ANXA5","ANXA6","APOE","APP","ARHGAP1","ARHGEF40","ARL1","ARL4A","ARMCX2","ARPC1B","ASPH","ATP10D","ATP1B1","ATP2B1","ATP2B4","ATP6V0E1","ATP8B2","ATXN1","B2M","BAG3","BGN","BMP5","BNC2","BOC","BTN3A2","C1orf198","C1orf54","C4orf32","C6orf120","CALD1","CALU","CAPN2","CAPN6","CBFB","CBLB","CCDC80","CD164","CD44","CD59","CD63","CDH11","CETN2","CFH","CFI","CILP","CKAP4","CLIC4","CMTM3","CMTM6","CNN3","COL11A1","COL12A1","COL1A1","COL27A1","COL3A1","COL4A1","COL4A2","COL5A1","COL5A2","COL6A1","COL6A2","COL6A3","COPA","CPED1","CPS1","CRABP2","CREB3L2","CREG1","CRELD2","CRISPLD1","CRTAP","CSRP1","CTDSP2","CTNNA1","CTSB","CTSC","CTSO","CXCL12","CYBRD1","CYFIP1","CYP26A1","CYR61","DCAF6","DDOST","DDR2","DESI2","DKK3","DLC1","DLX1","DLX2","DMD","DNAJC1","DNAJC10","DNAJC3","DNM3OS","DPY19L1","DSE","DUSP14","DUSP5","DUSP6","EDEM1","EDNRA","EFEMP2","EGFR","EGR1","EGR3","EHD2","ELAVL1","ELF1","ELK3","ELK4","EMILIN1","EMP1","ENAH","EPHA3","EPS8","ERBIN","ERLIN1","ERRFI1","ETS1","EVA1A","EXT1","EXTL2","F2R","F2RL2","FAM102B","FAM114A1","FAM120A","FAM129A","FAM3C","FAM43A","FAM46A","FAT1","FBN1","FBN2","FGFR1","FIBIN","FILIP1L","FKBP14","FLNA","FLRT2","FMOD","FN1","FNDC3B","FSTL1","FUCA2","FZD1","FZD2","FZD7","GABRR1","GALNT10","GAS1","GAS2","GDF15","GJA1","GNAI1","GNG12","GNS","GORAB","GPC6","GPR137B","GPX8","GRN","GSN","HES1","HEXB","HIBADH","HIPK3","HIST1H2AC","HIST1H2BK","HLA-A","HLA-B","HLA-C","HLA-F","HLX","HNMT","HOMER1","HS3ST3A1","HSP90B1","HSPA5","HSPB1","HTRA1","HYOU1","ID1","ID3","IFI16","IFITM2","IFITM3","IGF2R","IGFBP5","IGFBP6","IL13RA1","IL6ST","INSIG1","IQGAP2","ITGA10","ITGA4","ITGAV","ITGB1","ITM2B","ITM2C","ITPR1","ITPRIPL2","JAK1","JAM3","KANK2","KCNK2","KCTD12","KDELC2","KDELR2","KDELR3","KDM5B","KIAA1462","KIF13A","KIRREL","KLF10","KLF4","KLF6","L3HYPDH","LAMB1","LAMC1","LAMP1","LAPTM4A","LASP1","LATS2","LEPROT","LGALS1","LHFP","LHX8","LIFR","LIPA","LITAF","LIX1L","LMAN1","LMNA","LOXL2","LPP","LRP10","LRRC17","LRRC8C","LTBP1","LUZP1","MAGT1","MAML2","MAN2A1","MANF","MBD2","MBNL1","MBTPS1","MEOX1","MEOX2","MEST","MGAT2","MGP","MGST1","MICAL2","MMP2","MOB1A","MRC2","MXRA5","MYADM","MYDGF","MYL12A","MYL12B","MYLIP","NANS","NBR1","NEK7","NES","NFIA","NFIC","NID1","NID2","NOTCH2","NOTCH2NL","NPC2","NPTN","NQO1","NR3C1","NRP1","OGFRL1","OLFML2A","OLFML2B","OLFML3","OSTC","P4HA1","PALLD","PAPSS2","PCDH18","PCOLCE2","PCSK5","PDE3A","PDE7B","PDGFC","PDIA3","PDIA4","PDIA6","PDLIM1","PEA15","PEAK1","PHLDA3","PHLDB2","PHTF2","PIAS3","PLAGL1","PLEKHA2","PLEKHH2","PLK2","PLOD2","PLOD3","PLPP1","PLS3","PLSCR1","PLSCR4","PLXDC2","POLR2L","PON2","POSTN","PPIB","PPIC","PPT1","PRCP","PRDM6","PRDX4","PRDX6","PROM1","PRRX1","PTBP1","PTGER4","PTGFRN","PTN","PTPN14","PTPRG","PTPRK","PTRF","PXDC1","PXDN","PYGL","QKI","QSOX1","RAB13","RAB29","RAB31","RAP1A","RAP1B","RBMS1","RCN1","RECK","REST","RGL1","RGS10","RGS3","RHOC","RHOJ","RIN2","RIT1","RNFT1","RNH1","ROBO1","ROR1","RRBP1","S1PR3","SASH1","SCPEP1","SCRG1","SDC2","SDC4","SDCBP","SDF4","SEC14L1","SEL1L3","SEMA3C","SEMA3F","SEPT10","SERPINE2","SERPINH1","SFT2D1","SFT2D2","SGK1","SH3BGRL","SHC1","SHROOM3","SIX1","SIX4","SKIL","SLC16A4","SLC30A1","SLC30A7","SLC35F5","SLC38A2","SLC38A6","SLC39A14","SMAD3","SNAI2","SNAP23","SOSTDC1","SOX9","SPARC","SPARCL1","SPATA20","SPCS3","SPRED1","SPRY1","SPRY4","SPRY4-IT1","SQSTM1","SRPX","SSBP4","SSR1","SSR3","STAT1","STAT3","STEAP1","STK38L","SUCLG2","SURF4","SVIL","SYDE1","SYNJ2","SYPL1","TCF7L2","TFE3","TFPI","TGFB1I1","TGFBR2","THBS1","TIMP1","TJP1")


Hope this helps,

Rui Barradas

?s 14:50 de 13/07/2022, Richard O'Keefe escreveu:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      core_contingency
    

    

      
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Thank you everyone for the help. It is interesting that R sets a 
character limit on each line, but I am glad the solution is simple.

core_contingency

        
On 7/13/22 07:42, Rui Barradas wrote:

            

      
      
      
    

        

      
      
    

        
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      @vi@e@gross m@iii@g oii gm@ii@com
    

    

      
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If I follow this thread, it looks clear that the problem is superficial and not really about the c() function as it is below sea level.

Is this also a problem if you replace c() with max () or list() as I think it may be? Then it is more about what length the interpreter is able to handle everywhere or on your installation or memory constraints.

There are, of course, lots of ways to work around it and some have been mentioned, as you clearly have data.frames with underlying vectors that are millions of units long including with character data like yours.

I was able to reproduce your problem within RSTUDIO and noted the editor window actually cuts off the text and asks you to click to see more, which may be a hint. Have you tried a paste of this long thing directly to an R interpreter not through RSTUDIO?

I did an experiment and broke up the big monster that failed into multiple short lines and it works fine. It looks like a LINE LENGTH limit, not a statement limit.

So if your data was entered say like this:

MES=c(
  "A2M",
  "ABRACL",
  "ACADVL",
  "ACAP2",
  ...,
  "TIMP1",
  "TJP1"
  )

Then it should work for much larger amounts of data.

And, of course, you can enter multiple smaller units and concatenate them together in the code and remove the originals, as long as each unit was small enough. Reading the data in from a file also should bypass the issue if done right.

There is no reason every programmer should try to make everything a one-liner.


-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Ebert,Timothy Aaron
Sent: Wednesday, July 13, 2022 9:21 AM
To: Rui Barradas <ruipbarradas at sapo.pt>; core_contingency <ccontingency at gmail.com>; r-help at r-project.org
Subject: Re: [R] Does the function "c" have a character limit?

The limits to the size of vectors, matrices, data frames, lists, or other data structure does not have a simple answer.
1) 2^31 - 1  is the maximum number of rows. https://stackoverflow.com/questions/5233769/practical-limits-of-r-data-frame#:~:text=The%20number%20is%202%5E31,start%20collecting%20several%20of%20them.
2) help(Memory) suggests that the default limit for all variables is 6 Mb. The help page tells you how to change this.
Neither of these two factors have any bearing on this problem except that your vector is not close to these limits.

I got the same result you did when I entered your vector into my system (R 4.2 in RStudio, on 64 bit Windows). I shortened it by removing the first entry and it works.

I can copy the entire line into Microsoft Word, and count the number of characters (including spaces) and I get 4089. There were seven characters in the first entry including the comma and space. If I add seven spaces between MES and the equal sign I get the original outcome. So the limit is on the number of characters in the line. You can get more entries by shortening each entry, or fewer if each entry was longer.

As others have suggested, I would break the line into two pieces and then combine the pieces.

Tim



-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Rui Barradas
Sent: Wednesday, July 13, 2022 6:36 AM
To: core_contingency <ccontingency at gmail.com>; r-help at r-project.org
Subject: Re: [R] Does the function "c" have a character limit?

[External Email]

Hello,

This is documented behavior.
 From R-intro, last line of section 1.8 [1].


Command lines entered at the console are limited4 to about 4095 bytes (not characters).


The number 4 in limited4 is a footnote link:


some of the consoles will not allow you to enter more, and amongst those which do some will silently discard the excess and some will use it as the start of the next line.



Prof. Ripley called the r-devel mailing list's attention to this in August 2006 when the limit was 1024 [2], it was then increased to the current 4095. I remember seeing a limit of 2048 (?) but couldn't find where.


Try creating a file with your command as only content, then run


x <- readLines("rhelp.txt")
nchar(x)
# [1] 4096


You are above the limit by 1 byte.
Standard solutions are to break the command line, in your case into at least 2 lines, or to source the command from file, like David proposed.


[1]
https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dintro.html-23R-2Dcommands-5F003b-2Dcase-2Dsensitivity-2Detc&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=g5cbrpfyHaIN9sXycd_-f2iDsOcbuzLe2u3KjvQNm-0&e=
[2] https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_r-2Ddevel_2006-2DAugust_038985.html&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=B1YSca31vHlpy9WJG8o0MBTh7bX4v7M61eWfQ4tmdog&e=


Hope this helps,

Rui Barradas


?s 00:36 de 13/07/2022, core_contingency escreveu:

            

      
      
      
    

        

      
      
    

        
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=x5SJbPFsoqRiJYh7Y5B0QDKio2Wy4Je38lBBi99AbAE&e=
PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=bDsMNmn2OhMbQIvptul8Yl752vW7YkxJ0v91xFMGuYQo9NsNdzAp5k0CD2XzMc9x&s=lCG5D1ItMs8G_wkshvm4nBaVq4Ehy_zyq5mnp2zpt2Y&e=
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

  
  


  


      

    

    

      
      

        


  

        

      @vi@e@gross m@iii@g oii gm@ii@com
    

    

      
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To be clear, Everything has limits beyond which it is not expected to have to deal with. Buffers often pick a fixed size and often need complex code to keep grabbing a bigger size and copy and add more, or arrange various methods to link multiple memory areas into a growing whole, such as having an object with a list of smaller parts that are concatenated only when requested.

Many languages likely have similar constraints and one method hackers have used is to arrange to overflow such buffers carefully.

Have you verified if the normal stand-alone R interpreter accepts a longer one-liner and the cause may in RSTUDIO or whatever else you are using?

I will say the current design is flawed in that it does NOT give you an error, but since only some of the line is passed to the functionality then it is waiting for something that closes up the command such as a close parenthesis, or if it stops in middle of a string, also a close quote.

So, as we have said, just don't do that, albeit it is not necessarily easy to avoid when you have no idea the length of your data will be so high.


-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of core_contingency
Sent: Wednesday, July 13, 2022 11:50 AM
To: r-help at r-project.org
Subject: Re: [R] Does the function "c" have a character limit?

Thank you everyone for the help. It is interesting that R sets a character limit on each line, but I am glad the solution is simple.

core_contingency

        
On 7/13/22 07:42, Rui Barradas wrote: