title: R read.table() Some of the field separator and line breaks not recognized
body: <p>I ran into this issue while reading this tab delimited table <code>GO_MF.txt</code> into R. </p>
  
  <p>Here's part of my input:</p>
  
  <pre><code>YAL004W YAL004W Unknown                              
  YAL005C SSA1    unfolded protein binding    ATPase activity                          
  YAL007C ERP2    molecular_function                               
  YAL008W FUN14   molecular_function                               
  YAL009W SPO7    phosphoprotein phosphatase activity                              
  YAL012W CYS3    cystathionine gamma-lyase activity                               
  YAL013W DEP1    molecular_function                               
  YAL014C SYN8    SNAP receptor activity                               
  YAL017W PSK1    protein serine/threonine kinase activity
  </code></pre>
  
  <p>It is perfectly fine when I open it in excel: 3606 rows and up to 11 columns.</p>
  
  <p>However, when I tried to input this table into R using the following command:</p>
  
  <pre><code>no_col &lt;- max(count.fields("GO_MF.txt", sep = "\t"), na.rm=T)
  
  pop &lt;- read.table("GO_MF.txt", sep = "\t",fill = TRUE, as.is=T, col.names=1:no_col)
  </code></pre>
  
  <p>I found there were only 2284 obs. of 11 variables. When I <code>View(pop)</code> in Rstudio, I found that there's a cell that doesn't seem to recognize \t and \n (see below):
  my <code>pop[261,3]</code> is</p>
  
  <pre><code>5-flap endonuclease activity
  YBR229C ROT2    alpha-glucosidase activity
  YBR230C OM14    molecular_function
  YBR231C SWC5    molecular_function
  YBR232C YBR232C Unknown
  YBR233W PBP2    mRNA binding
  YBR234C ARC40   ubiquitin binding
  YBR235W VHC1    ion transmembrane transporter activity
  YBR236C ABD1    mRNA (guanine-N7-)-methyltransferase activity
  YBR237W PRP5    RNA-dependent ATPase activity
  YBR241C YBR241C substrate-specific transmembrane transporter activity
  YBR242W YBR242W molecular_function
  YBR243C ALG7    UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity
  YBR244W GPX2    phospholipid-hydroperoxide glutathione peroxidase activity  glutathione peroxidase activity
  YBR245C ISW1    nucleosome binding  ATPase activity rDNA binding    DNA binding
  YBR246W RRT2    molecular_function
  YBR248C HIS7    imidazoleglycerol-phosphate synthase activity
  YBR249C ARO4    3-deoxy-7-phosphoheptulonate synthase activity
  YBR250W SPO23   molecular_function
  YBR251W MRPS5   structural constituent of ribosome
  YBR253W SRB6    molecular_function
  YBR255W MTC4    molecular_function
  YBR258C SHG1    histone methyltransferase activity (H3-K4 specific)
  YBR260C RGD1    Rho GTPase activator activity   phosphatidylinositol-4,5-bisphosphate binding   phosphatidylinositol-3,5-bisphosphate binding   phosphatidylinositol-3-phosphate binding    phosphatidylinositol-4-phosphate binding    phosphatidylinositol-5-phosphate binding
  YBR261C TAE1    N-terminal protein N-methyltransferase activity
  YBR262C AIM5    molecular_function
  YBR263W SHM1    glycine hydroxymethyltransferase activity
  YBR264C YPT10   GTPase activity guanyl nucleotide binding
  YBR266C SLM6    Unknown
  YBR267W REI1    sequence-specific DNA binding
  YBR269C FMP21   molecular_function
  YBR270C BIT2    molecular_function
  YBR271W EFM2    S-adenosylmethionine-dependent methyltransferase activity   protein-lysine N-methyltransferase activity
  YBR273C UBX7    molecular_function
  YBR275C RIF1    telomeric DNA binding
  YBR277C YBR277C Unknown
  YBR278W DPB3    double-stranded DNA binding single-stranded DNA binding DNA-directed DNA polymerase activity
  YBR280C SAF1    ubiquitin-protein ligase activity
  YBR281C DUG2    peptidase activity  gamma-glutamyltransferase activity  omega peptidase activity
  YBR283C SSH1    protein transmembrane transporter activity  signal sequence binding
  YBR284W YBR284W AMP deaminase activity  molecular_function
  YBR287W YBR287W molecular_function
  YBR288C APM3    molecular_function
  YBR290W BSD2    protein binding
  YBR291C CTP1    tricarboxylate secondary active transmembrane transporter activity
  YBR293W VBA2    basic amino acid transmembrane transporter activity drug transmembrane transporter activity
  YBR294W SUL1    sulfate transmembrane transporter activity
  YBR297W MAL33   sequence-specific DNA binding transcription factor activity
  YBR298C MAL31   alpha-glucoside:hydrogen symporter activity
  YBR299W MAL32   sucrose alpha-glucosidase activity  alpha-glucosidase activity  maltose alpha-glucosidase activity
  YBR301W PAU24   molecular_function
  YCL001W RER1    molecular_function
  YCL002C YCL002C molecular_function
  YCL005W LDB16   molecular_function
  YCL008C STP22   ubiquitin binding
  YCL009C ILV6    enzyme regulator activity   acetolactate synthase activity
  YCL010C SGF29   methylated histone residue binding  RNA polymerase II transcription factor recruiting transcription factor activity
  YCL016C DCC1    molecular_function
  YCL023C YCL023C Unknown
  YCL029C BIK1    microtubule binding protein homodimerization activity
  YCL030C HIS4    phosphoribosyl-ATP diphosphatase activity   phosphoribosyl-AMP cyclohydrolase activity  histidinol dehydrogenase activity
  YCL033C MXR2    peptide-methionine (R)-S-oxide reductase activity
  YCL035C GRX1    disulfide oxidoreductase activity   glutathione transferase activity    glutathione peroxidase activity
  YCL037C SRO9    RNA binding
  YCL042W YCL042W molecular_function
  YCL044C MGR1    misfolded protein binding
  YCL046W YCL046W Unknown
  YCL047C POF1    ATPase activity
  YCL048W SPS22   molecular_function
  YCL049C YCL049C molecular_function
  YCL050C APA1    bis(5-nucleosyl)-tetraphosphatase activity
  </code></pre>
  
  <p>Any thoughts? </p>
  
  <p>Thanks in advance! </p>